Variant report

Variant	rs2571997
Chromosome Location	chr7:99514417-99514418
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99513401..99515939-chr7:99585193..99587203,2	K562	blood:
2	chr7:99514062..99516474-chr7:99604675..99606310,2	MCF-7	breast:
3	chr7:99497251..99500127-chr7:99514363..99515928,2	K562	blood:
4	chr7:99513066..99515933-chr7:99589978..99591835,2	K562	blood:
5	chr7:99436167..99437949-chr7:99514061..99515612,2	MCF-7	breast:
6	chr7:99513908..99516258-chr7:99668490..99670311,2	K562	blood:

Variant related genes	Relation type
ENSG00000235713	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1025576	0.92[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1048705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10808114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1121592	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12535919	1.00[YRI][hapmap]
rs12536945	1.00[YRI][hapmap]
rs13310903	0.82[ASN][1000 genomes]
rs1865472	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2060452	0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2082744	1.00[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2082745	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2247761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247762	0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2525541	0.84[CHB][hapmap]
rs2525542	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2525548	0.84[CHB][hapmap]
rs2527886	0.84[CHB][hapmap]
rs2527890	0.84[CHB][hapmap]
rs2527894	0.84[CHB][hapmap]
rs2527897	0.84[CHB][hapmap]
rs2527899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527900	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2527901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527902	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2527903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527904	0.97[ASN][1000 genomes]
rs2527906	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap]
rs2527908	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2527909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527911	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527912	0.96[ASN][1000 genomes]
rs2527913	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527915	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527916	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2527918	0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527919	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527920	0.96[ASN][1000 genomes]
rs2527921	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527925	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2527926	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2527927	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2571991	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2571992	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571993	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571994	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571995	0.97[ASN][1000 genomes]
rs2571996	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571998	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571999	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572000	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2572002	0.91[ASN][1000 genomes]
rs2572003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2572009	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2572010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2572011	0.94[ASN][1000 genomes]
rs2572012	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2572013	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2572015	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2572018	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2572019	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2572022	0.93[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2572023	0.81[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs2572024	0.82[AMR][1000 genomes]
rs4727439	0.96[ASN][1000 genomes]
rs474229	0.93[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs503115	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7781442	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7809747	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs2571997	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs2571997	TRIM4	cis	uninvolved skin	skin_eQTL
rs2571997	TRIM4	cis	Muscle Skeletal	GTEx
rs2571997	TRIM4	cis	cerebellum	SCAN
rs2571997	TRIM4	cis	Esophagus Mucosa	GTEx
rs2571997	TRIM4	cis	multi-tissue	Pritchard
rs2571997	TRIM4	cis	Artery Aorta	GTEx
rs2571997	TRIM4	cis	Whole Blood	GTEx
rs2571997	TRIM4	cis	Nerve Tibial	GTEx
rs2571997	TRIM4	cis	Liver	GTEx
rs2571997	TRIM4	cis	Artery Tibial	GTEx
rs2571997	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2571997	OR2AE1	cis	parietal	SCAN
rs2571997	PILRB	cis	multi-tissue	Pritchard
rs2571997	TRIM4	cis	normal skin	skin_eQTL
rs2571997	TRIM4	cis	parietal	SCAN
rs2571997	TRIM4	cis	Stomach	GTEx
rs2571997	TRIM4	cis	Esophagus Muscularis	GTEx
rs2571997	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2571997	OR2AE1	cis	cerebellum	SCAN
rs2571997	TRIM4	cis	lesional skin	skin_eQTL
rs2571997	TRIM4	cis	lymphoblastoid	seeQTL
rs2571997	TRIM4	cis	lung	GTEx
rs2571997	TRIM4	cis	Skin Sun Exposed Lower leg	GTEx
rs2571997	TRIM4	cis	Thyroid	GTEx
rs2571997	TRIM4	cis	Lymphoblastoid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99492600-99516600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:99503000-99516400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:99506400-99515800	Weak transcription	Fetal Heart	heart
4	chr7:99507000-99515000	Weak transcription	Psoas Muscle	Psoas
5	chr7:99507000-99515600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:99507200-99514600	Weak transcription	NHDF-Ad	bronchial
7	chr7:99507200-99516000	Weak transcription	Esophagus	oesophagus
8	chr7:99507200-99516400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:99507200-99516400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:99507400-99514600	Weak transcription	Fetal Brain Male	brain
11	chr7:99507400-99514600	Weak transcription	Fetal Kidney	kidney
12	chr7:99507400-99515800	Weak transcription	Colonic Mucosa	Colon
13	chr7:99507800-99515600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:99510200-99514800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr7:99511400-99514600	Genic enhancers	Dnd41	blood
16	chr7:99511600-99515000	Strong transcription	Fetal Thymus	thymus
17	chr7:99511800-99514600	Strong transcription	Fetal Muscle Leg	muscle
18	chr7:99511800-99515000	Strong transcription	Lung	lung
19	chr7:99511800-99515400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr7:99512000-99514800	Strong transcription	Fetal Lung	lung
21	chr7:99512000-99515000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr7:99512200-99515000	Strong transcription	Left Ventricle	heart
23	chr7:99512400-99514600	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:99512400-99515000	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr7:99512800-99514600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:99512800-99514600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:99512800-99514600	Strong transcription	Fetal Intestine Large	intestine
28	chr7:99512800-99514600	Strong transcription	Spleen	Spleen
29	chr7:99512800-99514600	Strong transcription	A549	lung
30	chr7:99512800-99514800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:99512800-99515000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:99512800-99515000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr7:99512800-99515200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr7:99512800-99515200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr7:99512800-99515400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:99513000-99514600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr7:99513000-99514800	Genic enhancers	HMEC	breast
38	chr7:99513000-99515000	Strong transcription	Primary B cells from cord blood	blood
39	chr7:99513000-99515200	Genic enhancers	Liver	Liver
40	chr7:99513200-99514600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr7:99513200-99514800	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr7:99513200-99515000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:99513200-99515200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr7:99513200-99515200	Genic enhancers	HepG2	liver
45	chr7:99513200-99515400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:99513200-99515600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr7:99513200-99515800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:99513400-99514600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:99513400-99514800	Strong transcription	Brain Anterior Caudate	brain
50	chr7:99513400-99514800	Genic enhancers	Hela-S3	cervix

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