Variant report

Variant	rs9829468
Chromosome Location	chr3:195641417-195641418
allele	A/T
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	POLR2A	chr3:195641359-195642404	H1-hESC	embryonic stem cell:	n/a	n/a
2	HA-E2F1	chr3:195641339-195642059	MCF-7	breast:	n/a	n/a
3	RCOR1	chr3:195641396-195642473	IMR90	lung:	n/a	n/a
4	TBP	chr3:195641379-195642278	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr3:195641408-195642453	SK-N-SH	brain:	n/a	chr3:195642073-195642082 chr3:195642067-195642085 chr3:195642062-195642083 chr3:195642069-195642082 chr3:195642068-195642084 chr3:195642070-195642080
6	RAD21	chr3:195641399-195642380	HCT-116	colon:	n/a	chr3:195642058-195642071 chr3:195641937-195641949 chr3:195642067-195642079 chr3:195642065-195642084 chr3:195642068-195642081 chr3:195641867-195641879 chr3:195642069-195642079
7	ESR1	chr3:195641380-195642161	T-47D	breast:	n/a	chr3:195641667-195641682
8	POLR2A	chr3:195641346-195642141	U87	brain:	n/a	n/a
9	TAF1	chr3:195641381-195642390	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:195639677..195641924-chr3:195679365..195681428,2	MCF-7	breast:
2	chr3:195640626..195643616-chr3:195648215..195651575,3	MCF-7	breast:
3	chr3:195586456..195588406-chr3:195641214..195643488,2	K562	blood:
4	chr3:195427135..195428717-chr3:195640369..195642128,2	MCF-7	breast:
5	chr3:195579682..195581641-chr3:195640524..195643207,2	MCF-7	breast:
6	chr3:195640609..195643340-chr3:195646974..195648992,2	MCF-7	breast:
7	chr3:195634985..195639388-chr3:195640414..195643668,6	K562	blood:

Variant related genes	Relation type
ENSG00000273009	TF binding region
TNK2	TF binding region
ENSG00000242086	Chromatin interaction
ENSG00000223783	Chromatin interaction
ENSG00000061938	Chromatin interaction
ENSG00000266730	Chromatin interaction
ENSG00000226155	Chromatin interaction
ENSG00000260261	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11706736	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13083487	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417901	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818146	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	nsv1011404	chr3:195627654-195656614	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9829468	MUC4	cis	Skin Sun Exposed Lower leg	GTEx
rs9829468	MUC4	cis	Nerve Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195637000-195641600	Weak transcription	Pancreas	Pancrea
2	chr3:195637000-195641600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:195637000-195641600	Weak transcription	NHDF-Ad	bronchial
4	chr3:195637200-195641600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:195637200-195641600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:195637200-195641600	Weak transcription	Brain Substantia Nigra	brain
7	chr3:195637200-195641600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:195637200-195641600	Weak transcription	Fetal Heart	heart
9	chr3:195637200-195641600	Weak transcription	HSMM	muscle
10	chr3:195637200-195641600	Weak transcription	HUVEC	blood vessel
11	chr3:195637200-195641600	Weak transcription	NH-A	brain
12	chr3:195637200-195641800	Weak transcription	Primary T cells from cord blood	blood
13	chr3:195637200-195643800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:195637400-195641600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:195637400-195641600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:195637400-195641600	Weak transcription	Primary B cells from cord blood	blood
17	chr3:195637400-195641600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:195637400-195641600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:195637400-195641600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:195637400-195641600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:195637400-195641600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:195637400-195641600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:195637400-195641600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:195637400-195641600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:195637400-195641600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:195637400-195641600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:195637400-195641600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:195637400-195641600	Weak transcription	Fetal Intestine Large	intestine
29	chr3:195637400-195641600	Weak transcription	Left Ventricle	heart
30	chr3:195637400-195641600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:195637400-195641600	Weak transcription	Right Atrium	heart
32	chr3:195637400-195641600	Weak transcription	Stomach Mucosa	stomach
33	chr3:195637400-195641600	Weak transcription	GM12878-XiMat	blood
34	chr3:195637400-195641600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:195637400-195641800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:195637400-195641800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:195637400-195641800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:195637600-195641600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr3:195637600-195641600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:195637600-195641600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:195637600-195641600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:195637600-195641600	Weak transcription	Dnd41	blood
43	chr3:195637600-195641800	Weak transcription	Spleen	Spleen
44	chr3:195637600-195642000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:195637600-195643600	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr3:195637800-195641600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:195637800-195641600	Weak transcription	Lung	lung
48	chr3:195637800-195641800	Weak transcription	Fetal Intestine Small	intestine
49	chr3:195638000-195641600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:195638000-195641600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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