Variant report

Variant	rs17169196
Chromosome Location	chr7:7681131-7681132
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	POLR2A	chr7:7679078-7681429	HepG2	liver:	n/a	n/a
2	CHD2	chr7:7679821-7681280	K562	blood:	n/a	n/a
3	GABPA	chr7:7679474-7681187	MCF-7	breast:	n/a	chr7:7680866-7680880
4	CHD2	chr7:7679573-7681141	Hela-S3	cervix:	n/a	n/a
5	SMARCC1	chr7:7679092-7681404	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr7:7678812-7681214	Hela-S3	cervix:	n/a	n/a
7	MAFK	chr7:7679337-7681481	Hela-S3	cervix:	n/a	chr7:7679735-7679746 chr7:7681124-7681133 chr7:7681140-7681155 chr7:7679683-7679700 chr7:7681123-7681133
8	MAX	chr7:7679392-7681227	MCF-7	breast:	n/a	n/a
9	POLR2A	chr7:7679481-7681387	K562	blood:	n/a	n/a
10	POLR2A	chr7:7679451-7681228	HepG2	liver:	n/a	n/a
11	CTCF	chr7:7681060-7681210	HPAF	blood vessel:	n/a	n/a
12	POLR2A	chr7:7679144-7681438	Hela-S3	cervix:	n/a	n/a
13	NR2F2	chr7:7679862-7681224	K562	blood:	n/a	n/a
14	RFX5	chr7:7680949-7681139	HepG2	liver:	n/a	n/a
15	SMC3	chr7:7680341-7681134	GM12878	blood:	n/a	n/a
16	TAF1	chr7:7679870-7681344	K562	blood:	n/a	n/a
17	RAD21	chr7:7680993-7681329	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr7:7681120-7681270	AG09319	gingival:	n/a	n/a
19	POLR2A	chr7:7679060-7681323	GM12891	blood:	n/a	n/a
20	EGR1	chr7:7679671-7681134	HCT-116	colon:	n/a	chr7:7680614-7680628 chr7:7680616-7680626 chr7:7680615-7680626 chr7:7679837-7679850 chr7:7680311-7680324 chr7:7680615-7680626 chr7:7680243-7680252 chr7:7680616-7680626
21	BHLHE40	chr7:7679570-7681170	GM12878	blood:	n/a	n/a
22	MAX	chr7:7679753-7681154	SK-N-SH	brain:	n/a	n/a
23	MXI1	chr7:7678754-7682381	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr7:7681020-7681170	BJ	skin:	n/a	n/a
25	SIN3AK20	chr7:7679531-7681354	MCF-7	breast:	n/a	n/a
26	POLR2A	chr7:7678993-7681329	GM12892	blood:	n/a	n/a
27	MAFK	chr7:7679518-7681304	HepG2	liver:	n/a	chr7:7679735-7679746 chr7:7681124-7681133 chr7:7681140-7681155 chr7:7679683-7679700 chr7:7681123-7681133
28	FOXM1	chr7:7679403-7681227	GM12878	blood:	n/a	n/a
29	POLR2A	chr7:7679110-7681220	GM12891	blood:	n/a	n/a
30	POLR2A	chr7:7679078-7681236	GM19099	blood:	n/a	n/a
31	MAX	chr7:7679479-7681139	GM12878	blood:	n/a	n/a
32	SMC3	chr7:7679466-7681325	Hela-S3	cervix:	n/a	n/a
33	MTA3	chr7:7678970-7681157	GM12878	blood:	n/a	n/a
34	TCF7L2	chr7:7679800-7681431	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr7:7679308-7681414	MCF10A-Er-Src	breast:	n/a	n/a
36	CTCF	chr7:7681080-7681230	NB4	blood:	n/a	n/a
37	CTCF	chr7:7681121-7681243	SK-N-SH_RA	brain:	n/a	n/a
38	RUNX3	chr7:7679507-7681178	GM12878	blood:	n/a	n/a
39	IRF1	chr7:7679563-7681285	K562	blood:	n/a	chr7:7680315-7680329 chr7:7680914-7680923
40	CTCF	chr7:7681040-7681190	WERI-Rb-1	eye:	n/a	n/a
41	CTCF	chr7:7680980-7681210	AG10803	skin:	n/a	n/a
42	POLR2A	chr7:7679068-7681273	GM12878	blood:	n/a	n/a
43	SMARCC2	chr7:7679484-7681488	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr7:7679656-7681186	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr7:7679722-7681205	HL-60	blood:	n/a	n/a
46	CHD1	chr7:7680589-7681443	H1-hESC	embryonic stem cell:	n/a	n/a
47	SIN3A	chr7:7679037-7681506	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr7:7679496-7681224	GM12878	blood:	n/a	n/a
49	MAFF	chr7:7680950-7681307	HepG2	liver:	n/a	n/a
50	POLR2A	chr7:7678988-7681348	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:7603046..7608569-chr7:7677123..7682101,8	MCF-7	breast:
2	chr7:7679018..7681584-chr7:8008760..8011156,4	K562	blood:
3	chr7:7680700..7683473-chr7:7685626..7688056,2	MCF-7	breast:
4	chr7:7673907..7678610-chr7:7678691..7681851,6	MCF-7	breast:
5	chr7:7623467..7625147-chr7:7680756..7682414,2	K562	blood:
6	chr7:7605040..7608458-chr7:7677009..7681661,8	K562	blood:
7	chr7:7605830..7608267-chr7:7679102..7681869,5	MCF-7	breast:
8	chr7:7672448..7678421-chr7:7678475..7681557,8	K562	blood:
9	chr7:7680697..7682834-chr7:8264362..8267648,3	K562	blood:
10	chr7:7678479..7681346-chr7:8300009..8302111,2	K562	blood:
11	chr16:58426233..58426947-chr7:7680660..7681169,2	Hela-S3	cervix:

Variant related genes	Relation type
RPA3	TF binding region
ENSG00000244239	Chromatin interaction
ENSG00000181938	Chromatin interaction
ENSG00000164654	Chromatin interaction
ENSG00000233108	Chromatin interaction
ENSG00000106415	Chromatin interaction
ENSG00000272894	Chromatin interaction
ENSG00000003147	Chromatin interaction
ENSG00000229970	Chromatin interaction
ENSG00000106399	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10234567	1.00[CHD][hapmap]
rs10249422	1.00[MEX][hapmap]
rs10251718	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10267405	1.00[MEX][hapmap]
rs10275145	1.00[MEX][hapmap]
rs10280185	1.00[MEX][hapmap]
rs10280723	1.00[MEX][hapmap]
rs11978595	1.00[MEX][hapmap]
rs12333875	1.00[MEX][hapmap]
rs12702633	1.00[JPT][hapmap]
rs13225575	1.00[JPT][hapmap]
rs13227682	1.00[JPT][hapmap]
rs13438746	1.00[MEX][hapmap]
rs17137419	1.00[MEX][hapmap]
rs17137697	1.00[CHD][hapmap]
rs17169197	0.92[YRI][hapmap]
rs17524233	1.00[JPT][hapmap]
rs17547731	1.00[JPT][hapmap]
rs2024374	1.00[JPT][hapmap]
rs28916005	1.00[JPT][hapmap]
rs28916280	1.00[CHD][hapmap]
rs6463702	1.00[JPT][hapmap]
rs6962939	1.00[JPT][hapmap]
rs6964593	1.00[JPT][hapmap]
rs6974820	1.00[JPT][hapmap]
rs6980052	1.00[JPT][hapmap]
rs7787580	1.00[JPT][hapmap]
rs7789164	1.00[JPT][hapmap]
rs7793870	1.00[JPT][hapmap]
rs7805479	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv1034199	chr7:7617835-7691176	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv606044	chr7:7652372-7727101	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv887479	chr7:7681131-7779091	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7678600-7681200	Active TSS	HMEC	breast
2	chr7:7678800-7681200	Active TSS	A549	lung
3	chr7:7678800-7681400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr7:7678800-7681400	Active TSS	K562	blood
5	chr7:7678800-7681600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:7679000-7681200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:7679000-7681200	Active TSS	Brain Angular Gyrus	brain
8	chr7:7679000-7681200	Active TSS	Fetal Muscle Trunk	muscle
9	chr7:7679000-7681200	Active TSS	Psoas Muscle	Psoas
10	chr7:7679000-7681200	Active TSS	GM12878-XiMat	blood
11	chr7:7679000-7681400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr7:7679000-7681400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr7:7679000-7681400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:7679000-7681400	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr7:7679000-7681400	Active TSS	NHLF	lung
16	chr7:7679000-7681600	Active TSS	H1 Cell Line	embryonic stem cell
17	chr7:7679000-7681600	Active TSS	H9 Cell Line	embryonic stem cell
18	chr7:7679000-7681600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:7679000-7681600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:7679000-7681600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:7679000-7681800	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr7:7679000-7682000	Active TSS	Fetal Intestine Small	intestine
23	chr7:7679200-7681200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr7:7679200-7681200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr7:7679200-7681200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr7:7679200-7681200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr7:7679200-7681200	Active TSS	Muscle Satellite Cultured Cells	--
28	chr7:7679200-7681200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:7679200-7681200	Active TSS	Lung	lung
30	chr7:7679200-7681200	Active TSS	NHDF-Ad	bronchial
31	chr7:7679200-7681400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:7679200-7681400	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr7:7679200-7681400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr7:7679200-7681400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:7679200-7681400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:7679200-7681400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:7679200-7681400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:7679200-7681400	Active TSS	Esophagus	oesophagus
39	chr7:7679200-7681400	Active TSS	Ovary	ovary
40	chr7:7679200-7681400	Active TSS	Stomach Mucosa	stomach
41	chr7:7679200-7681400	Active TSS	HSMMtube	muscle
42	chr7:7679200-7681600	Active TSS	Right Atrium	heart
43	chr7:7679200-7681600	Active TSS	NHEK	skin
44	chr7:7679200-7682000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:7679400-7681200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:7679400-7681200	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr7:7679400-7681200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr7:7679400-7681200	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr7:7679400-7681200	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr7:7679400-7681200	Active TSS	Fetal Brain Female	brain

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