Variant report

Variant	rs2881373
Chromosome Location	chr4:159092633-159092634
allele	C/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	chr4:159091271-159092832	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:159091644-159092718	HepG2	liver:	n/a	n/a
3	SIN3AK20	chr4:159092425-159092702	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr4:159092191-159092793	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr4:159091652-159092689	MCF-7	breast:	n/a	n/a
6	SIN3AK20	chr4:159091468-159092840	MCF-7	breast:	n/a	n/a
7	FOS	chr4:159092413-159092824	MCF10A-Er-Src	breast:	n/a	chr4:159092778-159092786
8	REST	chr4:159092362-159092773	PFSK-1	brain:	n/a	n/a
9	FOS	chr4:159092370-159092847	MCF10A-Er-Src	breast:	n/a	chr4:159092835-159092844 chr4:159092778-159092786
10	STAT3	chr4:159092585-159092648	MCF10A-Er-Src	breast:	n/a	n/a
11	GATA2	chr4:159092285-159092816	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr4:159090972-159092820	PBDE	blood:	n/a	n/a
13	POLR2A	chr4:159092300-159092678	HepG2	liver:	n/a	n/a
14	FOS	chr4:159092380-159092907	HUVEC	blood vessel:	n/a	chr4:159092835-159092844 chr4:159092778-159092786
15	HEY1	chr4:159092291-159092700	HepG2	liver:	n/a	n/a
16	POLR2A	chr4:159091657-159092755	HepG2	liver:	n/a	n/a
17	MAX	chr4:159091682-159092769	MCF-7	breast:	n/a	n/a
18	POLR2A	chr4:159092262-159092861	HUVEC	blood vessel:	n/a	n/a
19	STAT3	chr4:159092485-159092892	MCF10A-Er-Src	breast:	n/a	chr4:159092748-159092759 chr4:159092750-159092758
20	POLR2A	chr4:159090562-159092956	HUVEC	blood vessel:	n/a	n/a
21	STAT3	chr4:159092431-159092962	MCF10A-Er-Src	breast:	n/a	chr4:159092748-159092759 chr4:159092750-159092758
22	POLR2A	chr4:159091061-159092865	HUVEC	blood vessel:	n/a	n/a
23	MYC	chr4:159092358-159093098	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr4:159091619-159092711	MCF-7	breast:	n/a	n/a
25	MYC	chr4:159091731-159092644	MCF-7	breast:	n/a	n/a
26	POLR2A	chr4:159091688-159092742	MCF-7	breast:	n/a	n/a
27	POLR2A	chr4:159092520-159092748	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr4:159092009-159092746	ProgFib	skin:	n/a	n/a
29	REST	chr4:159092239-159092721	MCF-7	breast:	n/a	n/a
30	E2F4	chr4:159092431-159092650	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr4:159092323-159092740	HepG2	liver:	n/a	n/a
32	POLR2A	chr4:159092273-159092654	HUVEC	blood vessel:	n/a	n/a
33	MYC	chr4:159092346-159092919	MCF10A-Er-Src	breast:	n/a	n/a
34	STAT3	chr4:159092368-159092842	MCF10A-Er-Src	breast:	n/a	chr4:159092748-159092759 chr4:159092750-159092758

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159090875..159093077-chr4:159130370..159132510,2	MCF-7	breast:

Variant related genes	Relation type
FAM198B	TF binding region
ENSG00000248429	TF binding region
ENSG00000164124	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10008208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10012339	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10018872	1.00[JPT][hapmap]
rs10024133	1.00[JPT][hapmap]
rs10028490	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10517689	1.00[JPT][hapmap]
rs11100151	1.00[JPT][hapmap]
rs11731973	0.81[CEU][hapmap]
rs11938464	1.00[JPT][hapmap]
rs12502811	1.00[JPT][hapmap]
rs12511679	1.00[JPT][hapmap]
rs12645131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12648410	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320370	1.00[JPT][hapmap]
rs1320371	1.00[JPT][hapmap]
rs14202	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1879659	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2346320	1.00[JPT][hapmap]
rs2346321	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2346381	1.00[JPT][hapmap]
rs2346776	1.00[JPT][hapmap]
rs2346780	1.00[JPT][hapmap]
rs2346781	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2346784	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4234917	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4309890	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4317248	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4345228	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4389619	0.93[CEU][hapmap]
rs4391084	1.00[JPT][hapmap]
rs4472184	1.00[JPT][hapmap]
rs4501266	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4582199	1.00[JPT][hapmap]
rs4627913	1.00[JPT][hapmap]
rs4690893	1.00[JPT][hapmap]
rs4691455	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4691456	1.00[JPT][hapmap]
rs4691457	1.00[JPT][hapmap]
rs4691458	1.00[JPT][hapmap]
rs4691461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4691462	1.00[JPT][hapmap]
rs4691463	1.00[JPT][hapmap]
rs4691464	1.00[JPT][hapmap]
rs4691465	1.00[JPT][hapmap]
rs4691467	1.00[JPT][hapmap]
rs6536299	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6812635	1.00[JPT][hapmap]
rs6820988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6821598	1.00[JPT][hapmap]
rs6830702	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6832099	1.00[JPT][hapmap]
rs6833198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6834164	1.00[JPT][hapmap]
rs6844920	0.82[CHB][hapmap]
rs6849902	1.00[JPT][hapmap]
rs6852646	1.00[JPT][hapmap]
rs6852878	0.83[AMR][1000 genomes]
rs6855420	1.00[JPT][hapmap]
rs7671094	1.00[JPT][hapmap]
rs7671501	1.00[JPT][hapmap]
rs7671934	1.00[JPT][hapmap]
rs7695599	1.00[JPT][hapmap]
rs8370	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2881373	DKFZp434L142	cis	multi-tissue	Pritchard
rs2881373	FLJ11155	cis	multi-tissue	Pritchard
rs2881373	RP11-597D13.9	cis	Heart Left Ventricle	GTEx
rs2881373	TMEM144	cis	Whole Blood	GTEx
rs2881373	FAM198B	cis	Whole Blood	GTEx
rs2881373	TMEM144	cis	Artery Aorta	GTEx
rs2881373	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs2881373	TMEM144	cis	Nerve Tibial	GTEx
rs2881373	RP11-597D13.9	cis	Esophagus Muscularis	GTEx
rs2881373	TMEM144	cis	Esophagus Muscularis	GTEx
rs2881373	RP11-597D13.7	cis	Nerve Tibial	GTEx
rs2881373	FAM198B	cis	parietal	SCAN
rs2881373	LOC646890	cis	multi-tissue	Pritchard

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159078600-159094000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:159085000-159095200	Active TSS	Aorta	Aorta
3	chr4:159085200-159094000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr4:159085400-159095000	Active TSS	Right Atrium	heart
5	chr4:159085600-159095000	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr4:159086400-159093200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:159088400-159094400	Active TSS	Right Ventricle	heart
8	chr4:159088600-159094400	Active TSS	Fetal Heart	heart
9	chr4:159089000-159094600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr4:159089200-159094200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr4:159089600-159094000	Active TSS	Colon Smooth Muscle	Colon
12	chr4:159089600-159094200	Active TSS	Colonic Mucosa	Colon
13	chr4:159089800-159093800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:159089800-159094600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:159090000-159093800	Active TSS	Brain Anterior Caudate	brain
16	chr4:159090000-159094000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:159090200-159093400	Active TSS	HUVEC	blood vessel
18	chr4:159090200-159094200	Active TSS	Left Ventricle	heart
19	chr4:159090200-159094200	Active TSS	Psoas Muscle	Psoas
20	chr4:159090200-159094200	Active TSS	HSMM	muscle
21	chr4:159090200-159094400	Active TSS	Fetal Intestine Large	intestine
22	chr4:159090200-159095000	Active TSS	HSMMtube	muscle
23	chr4:159090400-159094400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:159090600-159093000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr4:159090800-159092800	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr4:159090800-159094000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:159090800-159094000	Active TSS	Brain Substantia Nigra	brain
28	chr4:159091000-159093800	Active TSS	Primary monocytes fromperipheralblood	blood
29	chr4:159091000-159094000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:159091000-159094000	Active TSS	Fetal Kidney	kidney
31	chr4:159091000-159094000	Active TSS	Monocytes-CD14+_RO01746	blood
32	chr4:159091000-159094400	Active TSS	Fetal Intestine Small	intestine
33	chr4:159091600-159092800	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr4:159091600-159092800	Flanking Active TSS	Placenta	Placenta
35	chr4:159091600-159093200	Weak transcription	NH-A	brain
36	chr4:159091600-159093800	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr4:159091800-159092800	Active TSS	Liver	Liver
38	chr4:159091800-159093200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr4:159091800-159093800	Active TSS	Brain Angular Gyrus	brain
40	chr4:159091800-159093800	Active TSS	Brain Cingulate Gyrus	brain
41	chr4:159092000-159093200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:159092000-159093600	Bivalent Enhancer	Primary B cells from cord blood	blood
43	chr4:159092200-159092800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:159092200-159093000	Flanking Active TSS	NHEK	skin
45	chr4:159092200-159093200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:159092400-159092800	Flanking Active TSS	Fetal Lung	lung
47	chr4:159092400-159093200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:159092400-159093800	Active TSS	Placenta Amnion	Placenta Amnion
49	chr4:159092400-159093800	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr4:159092400-159093800	Weak transcription	Small Intestine	intestine

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