Variant report

Variant	rs6709571
Chromosome Location	chr2:98531626-98531627
allele	C/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	RUNX3	chr2:98531235-98531722	GM12878	blood:	n/a	n/a
2	RUNX3	chr2:98531291-98531701	GM12878	blood:	n/a	n/a
3	BATF	chr2:98531307-98531628	GM12878	blood:	n/a	n/a
4	EBF1	chr2:98530136-98531658	GM12878	blood:	n/a	chr2:98530345-98530354 chr2:98530344-98530354 chr2:98530343-98530354 chr2:98530345-98530354 chr2:98530343-98530356
5	STAT3	chr2:98531427-98531627	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98525688..98528111-chr2:98529878..98532703,2	MCF-7	breast:

Variant related genes	Relation type
RNU7-96P	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10176201	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10182941	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10200949	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10211231	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1071885	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865055	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11123924	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11123949	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123966	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11690482	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11693874	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11888323	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11899171	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12712123	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12712174	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712176	0.81[ASN][1000 genomes]
rs13003978	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13006817	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13008503	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13010946	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13022778	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13034644	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1317178	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13405546	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1466020	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1466924	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1503200	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1922280	0.98[ASN][1000 genomes]
rs1922282	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017028	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2091772	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2100058	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2141862	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279825	0.83[ASN][1000 genomes]
rs2279826	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2305142	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs2309316	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2309317	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2309356	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3762593	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4274643	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4560167	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5865	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs6543108	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6543109	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6543161	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6543177	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6543202	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6543210	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6707924	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6710813	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6712517	0.84[CEU][hapmap]
rs6719556	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6723466	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6723653	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6744331	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6748809	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6748927	0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs7558931	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs7561104	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7562695	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7567397	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7574437	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7577886	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7582664	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7586210	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7598116	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7602412	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7605180	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs930607	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9308862	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs956696	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9973416	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6709571	ZAP70	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98503800-98536400	Weak transcription	HSMMtube	muscle
2	chr2:98504000-98533800	Weak transcription	Spleen	Spleen
3	chr2:98504000-98538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:98504000-98540600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:98504000-98540800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:98504600-98540800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:98504600-98552200	Weak transcription	NHLF	lung
8	chr2:98507600-98535000	Weak transcription	Brain Anterior Caudate	brain
9	chr2:98509000-98536400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:98515800-98540800	Weak transcription	Aorta	Aorta
11	chr2:98516400-98534600	Weak transcription	A549	lung
12	chr2:98519600-98541600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:98519800-98538600	Weak transcription	Gastric	stomach
14	chr2:98520200-98546000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:98520200-98552200	Weak transcription	Brain Angular Gyrus	brain
16	chr2:98520600-98550600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:98520800-98540400	Weak transcription	Lung	lung
18	chr2:98521200-98532800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:98521800-98540400	Weak transcription	Colonic Mucosa	Colon
20	chr2:98523200-98536200	Weak transcription	Ovary	ovary
21	chr2:98523200-98540600	Weak transcription	Right Ventricle	heart
22	chr2:98523400-98536000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:98523400-98536400	Weak transcription	Esophagus	oesophagus
24	chr2:98523400-98536600	Weak transcription	HSMM	muscle
25	chr2:98523400-98540600	Weak transcription	Fetal Brain Female	brain
26	chr2:98523400-98545800	Weak transcription	Fetal Kidney	kidney
27	chr2:98523400-98546200	Weak transcription	HUVEC	blood vessel
28	chr2:98523800-98537600	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:98524400-98532600	Weak transcription	HMEC	breast
30	chr2:98524600-98552600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:98524800-98532400	Enhancers	Primary B cells from peripheral blood	blood
32	chr2:98524800-98532400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:98524800-98540800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:98524800-98552200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:98525000-98532400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:98525000-98534000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:98525000-98536000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:98525000-98536200	Weak transcription	Placenta	Placenta
39	chr2:98525000-98538600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr2:98525000-98539200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:98525000-98540600	Weak transcription	Adipose Nuclei	Adipose
42	chr2:98525000-98551600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:98525200-98532600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:98525200-98538800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:98525200-98547400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:98525600-98531800	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:98525600-98539200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:98525600-98548200	Weak transcription	Pancreas	Pancrea
49	chr2:98525800-98540800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr2:98526000-98532600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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