Variant report

Variant	rs1796043
Chromosome Location	chr2:97623413-97623414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr2:97623151-97623421	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr2:97623039-97623503	H1-hESC	embryonic stem cell:	n/a	chr2:97623262-97623271
3	SIN3A	chr2:97623059-97623489	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr2:97623329-97623427	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:97480973..97483903-chr2:97621623..97628750,6	MCF-7	breast:
2	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
3	chr2:97537658..97539492-chr2:97622900..97626326,3	K562	blood:
4	chr2:97302399..97305389-chr2:97622198..97624620,2	K562	blood:
5	chr2:97536159..97540837-chr2:97622900..97627821,5	K562	blood:
6	chr2:97623151..97625255-chr2:97629201..97631510,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNA5SP101	TF binding region
ENSG00000213337	Chromatin interaction
ENSG00000168763	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000114982	Chromatin interaction
ENSG00000163126	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10874468	0.97[GIH][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs11164113	0.86[AMR][1000 genomes]
rs1148592	1.00[JPT][hapmap]
rs1148595	1.00[JPT][hapmap]
rs11676858	1.00[ASW][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes]
rs11680224	0.86[AMR][1000 genomes]
rs11688134	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1257006	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1257010	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1257013	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1257014	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1257021	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1257022	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1257026	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1257084	1.00[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1257089	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1257101	0.85[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs1257117	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12997297	0.84[AMR][1000 genomes]
rs13009659	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1669760	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1796025	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1796048	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1796050	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2443873	0.93[JPT][hapmap]
rs2463904	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4063952	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6730782	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7569432	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs9324210	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking 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 miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv1001432	chr2:97591069-97671395	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	esv32727	chr2:97616488-97643975	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1796043	ANKRD36B	cis	Thyroid	GTEx
rs1796043	TGFBR3	trans	lymphoblastoid	seeQTL
rs1796043	ACTR1B	cis	cerebellum	SCAN
rs1796043	CIAO1	cis	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97619600-97628400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:97620200-97625600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:97620400-97625000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:97620400-97625200	Weak transcription	Brain Angular Gyrus	brain
5	chr2:97620400-97625200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:97620400-97625200	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:97620400-97625800	Weak transcription	Primary T cells from cord blood	blood
8	chr2:97620400-97625800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:97620400-97629400	Weak transcription	Fetal Intestine Large	intestine
10	chr2:97620600-97625200	Weak transcription	Brain Substantia Nigra	brain
11	chr2:97620600-97625600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:97620600-97625600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:97620600-97625600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:97620600-97625600	Weak transcription	Fetal Brain Female	brain
15	chr2:97620600-97626000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:97620600-97626000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:97620600-97628200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:97620800-97625600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:97620800-97625600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:97620800-97625600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:97620800-97625600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:97620800-97625600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:97620800-97626000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:97620800-97626000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:97620800-97626000	Weak transcription	Stomach Mucosa	stomach
26	chr2:97620800-97627600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:97620800-97629600	Weak transcription	Fetal Intestine Small	intestine
28	chr2:97620800-97643600	Weak transcription	Right Atrium	heart
29	chr2:97621000-97626000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:97621000-97626400	Weak transcription	GM12878-XiMat	blood
31	chr2:97621400-97623600	Enhancers	Spleen	Spleen
32	chr2:97621800-97625600	Weak transcription	Colonic Mucosa	Colon
33	chr2:97622000-97625400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:97622000-97625600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:97622000-97626000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:97622000-97626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:97622200-97626000	Weak transcription	Ovary	ovary
38	chr2:97622200-97626000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:97622800-97623600	Enhancers	H1 Cell Line	embryonic stem cell
40	chr2:97622800-97623600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:97622800-97623600	Enhancers	K562	blood
42	chr2:97622800-97623800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr2:97622800-97623800	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr2:97622800-97623800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr2:97622800-97623800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr2:97623000-97623600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:97623000-97623600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:97623000-97623600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:97623000-97623800	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr2:97623000-97623800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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