Variant report

Variant	rs9871110
Chromosome Location	chr3:195625326-195625327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr3:195624976-195625327	HL-60	blood:	n/a	n/a
2	ZNF263	chr3:195624816-195625349	HEK293-T-REx	kidney:	n/a	n/a
3	SIN3AK20	chr3:195623824-195625518	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:195623300..195626521-chr3:195635118..195637851,4	K562	blood:
2	chr3:195618618..195620399-chr3:195623360..195626055,3	MCF-7	breast:
3	chr3:195585410..195592750-chr3:195621468..195626254,9	MCF-7	breast:

Variant related genes	Relation type
TNK2	TF binding region
ENSG00000061938	Chromatin interaction
ENSG00000223783	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1871529	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3747671	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3747672	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6421308	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs745497	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs881753	0.80[TSI][hapmap]
rs9829709	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:37 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
2	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
3	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv1001387	chr3:195186128-195661538	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
5	nsv428102	chr3:195201080-195829426	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv428430	chr3:195201080-195829426	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv1006217	chr3:195312401-195643229	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
8	nsv536882	chr3:195312401-195643229	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
9	esv1813494	chr3:195325408-195628669	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
10	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
11	nsv1006165	chr3:195383130-195777211	Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
12	nsv471621	chr3:195417664-195795474	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
13	nsv878157	chr3:195421983-195628636	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
14	esv2751988	chr3:195433543-195651349	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
15	esv2756651	chr3:195433543-195696720	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
16	nsv432528	chr3:195433543-195696720	Enhancers Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
17	esv2754016	chr3:195433543-195753766	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
18	nsv822410	chr3:195438740-195725565	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
19	nsv1003062	chr3:195473784-195630700	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
20	nsv878162	chr3:195475989-195641908	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
21	nsv878163	chr3:195477791-195641908	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
22	nsv997893	chr3:195501392-195642192	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
23	nsv1005193	chr3:195526571-195709662	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
24	nsv878166	chr3:195550366-195628636	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
25	nsv878167	chr3:195550366-195637439	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
26	nsv878168	chr3:195553259-195644332	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
27	nsv1002591	chr3:195564086-195643229	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
28	nsv530397	chr3:195565159-195740416	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
29	nsv878169	chr3:195571024-195628636	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
30	nsv593056	chr3:195571024-195656731	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
31	nsv1007235	chr3:195582468-195651911	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
32	nsv1002629	chr3:195582468-195769275	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
33	esv1811906	chr3:195598137-195637469	Active TSS Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
34	nsv1014602	chr3:195606770-195661538	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
35	nsv829827	chr3:195608866-195760829	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
36	nsv469518	chr3:195623722-195795474	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
37	nsv482784	chr3:195623722-195795474	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9871110	PIGZ	cis	cerebellum	SCAN
rs9871110	PDCD6	Cis_chr	lymphoblastoid	RTeQTL
rs9871110	KIAA0226	cis	cerebellum	SCAN
rs9871110	MUC20	cis	multi-tissue	Pritchard
rs9871110	LOC152217	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195623200-195625600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:195623200-195633000	Weak transcription	Small Intestine	intestine
3	chr3:195623400-195625400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
4	chr3:195623400-195625400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr3:195623400-195625400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:195623400-195625400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:195623400-195625400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:195623400-195625400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:195623400-195625400	Enhancers	Esophagus	oesophagus
10	chr3:195623400-195625400	Enhancers	Lung	lung
11	chr3:195623400-195625600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:195623400-195625600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:195623400-195625600	Enhancers	Left Ventricle	heart
14	chr3:195623400-195625600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr3:195623400-195625600	Enhancers	Thymus	Thymus
16	chr3:195623400-195627000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:195623400-195627800	Enhancers	Fetal Thymus	thymus
18	chr3:195623400-195632400	Enhancers	Primary B cells from peripheral blood	blood
19	chr3:195623600-195625400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:195623600-195625400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr3:195623600-195625400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr3:195623600-195625400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr3:195623600-195625400	Enhancers	Fetal Muscle Trunk	muscle
24	chr3:195623600-195625600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr3:195623600-195625800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr3:195623600-195625800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr3:195623600-195626000	Enhancers	Placenta	Placenta
28	chr3:195623600-195627200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr3:195623600-195629400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr3:195623600-195631000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:195623800-195625400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr3:195623800-195625400	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr3:195623800-195625400	Enhancers	A549	lung
34	chr3:195623800-195625400	Enhancers	HSMM	muscle
35	chr3:195623800-195625400	Enhancers	HUVEC	blood vessel
36	chr3:195623800-195625400	Enhancers	NH-A	brain
37	chr3:195623800-195625600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:195623800-195625600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr3:195623800-195625600	Enhancers	Fetal Heart	heart
40	chr3:195623800-195625600	Enhancers	Fetal Lung	lung
41	chr3:195623800-195625600	Enhancers	Fetal Muscle Leg	muscle
42	chr3:195623800-195625600	Enhancers	GM12878-XiMat	blood
43	chr3:195623800-195625600	Enhancers	NHEK	skin
44	chr3:195623800-195625800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:195623800-195625800	Enhancers	HMEC	breast
46	chr3:195623800-195627000	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr3:195623800-195630400	Enhancers	Primary B cells from cord blood	blood
48	chr3:195623800-195630800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:195623800-195631000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:195623800-195633000	Weak transcription	Fetal Brain Female	brain

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