Variant report

Variant	rs4150402
Chromosome Location	chr2:128050134-128050135
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	chr2:128050069-128050235	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:128049947-128050539	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:128050006-128050236	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:128045827..128047881-chr2:128049026..128051803,2	MCF-7	breast:
2	chr2:128047217..128049031-chr2:128049443..128051921,3	MCF-7	breast:
3	chr2:128050076..128053017-chr2:128173952..128176764,3	MCF-7	breast:

Variant related genes	Relation type
ERCC3	TF binding region
ENSG00000115718	Chromatin interaction
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1011019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10496661	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11541137	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11679414	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11680877	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680949	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11683986	1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs11691916	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692990	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030463	1.00[ASN][1000 genomes]
rs1504135	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1518760	1.00[ASN][1000 genomes]
rs1568278	1.00[ASN][1000 genomes]
rs17261845	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17261859	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2069895	1.00[ASN][1000 genomes]
rs2069898	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2069902	1.00[ASN][1000 genomes]
rs2069904	1.00[CHB][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];1.00[ASN][1000 genomes]
rs2069919	1.00[ASN][1000 genomes]
rs2896979	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334151	1.00[ASN][1000 genomes]
rs334152	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334156	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334157	1.00[ASN][1000 genomes]
rs334158	1.00[ASN][1000 genomes]
rs334159	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334160	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3732209	0.86[ASW][hapmap];0.81[CEU][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs3958415	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150400	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4150404	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4150416	1.00[ASN][1000 genomes]
rs4150421	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150476	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150499	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150523	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4536600	0.81[MEX][hapmap]
rs4662713	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662718	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662719	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662720	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55998444	1.00[ASN][1000 genomes]
rs56273408	1.00[ASN][1000 genomes]
rs5937	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs59378658	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61422716	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62157508	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6430933	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6430936	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6430938	1.00[ASN][1000 genomes]
rs6731332	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6733478	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738690	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744237	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72845944	1.00[ASN][1000 genomes]
rs72845975	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845976	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845979	0.83[EUR][1000 genomes]
rs72845982	0.83[EUR][1000 genomes]
rs72845991	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845993	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845997	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72846002	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72848604	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72848612	1.00[ASN][1000 genomes]
rs72848615	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72848616	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72848618	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556756	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7562428	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590030	0.86[ASW][hapmap];0.81[CEU][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7607907	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs777569	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4150402	BIN1	cis	parietal	SCAN
rs4150402	ERCC3	cis	Nerve Tibial	GTEx
rs4150402	ERCC3	cis	Esophagus Muscularis	GTEx
rs4150402	ERCC3	cis	Adipose Subcutaneous	GTEx
rs4150402	ERCC3	cis	parietal	SCAN
rs4150402	MAP3K2	cis	multi-tissue	Pritchard
rs4150402	ERCC3	cis	cerebellum	SCAN
rs4150402	ERCC3	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128023400-128050400	Strong transcription	Liver	Liver
2	chr2:128024200-128050600	Strong transcription	Fetal Intestine Large	intestine
3	chr2:128024400-128050200	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr2:128024400-128050200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:128024400-128050200	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:128024400-128050400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:128024400-128050400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:128024400-128050400	Strong transcription	Thymus	Thymus
9	chr2:128024400-128050800	Strong transcription	Fetal Thymus	thymus
10	chr2:128024600-128050200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr2:128024600-128050200	Strong transcription	Adipose Nuclei	Adipose
12	chr2:128024800-128050200	Strong transcription	Brain Anterior Caudate	brain
13	chr2:128024800-128050200	Strong transcription	Brain Hippocampus Middle	brain
14	chr2:128024800-128050200	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:128024800-128050200	Strong transcription	Stomach Smooth Muscle	stomach
16	chr2:128024800-128050400	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr2:128024800-128050400	Strong transcription	Osteobl	bone
18	chr2:128025000-128050600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:128025200-128050200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:128033800-128050400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:128034200-128050200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:128034200-128050200	Strong transcription	K562	blood
23	chr2:128034400-128050200	Strong transcription	HUVEC	blood vessel
24	chr2:128034800-128050400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:128036600-128050200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:128036600-128050800	Weak transcription	Right Atrium	heart
27	chr2:128036800-128050200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:128037400-128050400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:128037400-128050400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:128037400-128050600	Strong transcription	Right Ventricle	heart
31	chr2:128039200-128050200	Strong transcription	Brain Substantia Nigra	brain
32	chr2:128039200-128050400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:128039200-128050400	Strong transcription	Ovary	ovary
34	chr2:128039200-128050600	Strong transcription	NHEK	skin
35	chr2:128039400-128050200	Strong transcription	Placenta	Placenta
36	chr2:128039800-128050400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:128039800-128050400	Strong transcription	Fetal Kidney	kidney
38	chr2:128040200-128050400	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr2:128040200-128050600	Strong transcription	Colon Smooth Muscle	Colon
40	chr2:128040400-128050400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr2:128040800-128050200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:128041000-128050200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:128041200-128050200	Strong transcription	NHDF-Ad	bronchial
44	chr2:128041400-128050400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:128041400-128050400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:128041800-128050200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr2:128041800-128050400	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr2:128041800-128050400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:128041800-128050400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:128041800-128050400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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