Variant report

Variant	rs2198511
Chromosome Location	chr1:77834367-77834368
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	GATA3	chr1:77834280-77834443	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
AK5	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10493605	1.00[ASW][hapmap]
rs10873935	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11162325	0.85[ASN][1000 genomes]
rs11162326	0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs11162327	0.95[ASN][1000 genomes]
rs11162329	0.88[ASN][1000 genomes]
rs11584919	1.00[YRI][hapmap]
rs11585455	0.92[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs11590456	1.00[YRI][hapmap]
rs12043793	0.88[ASN][1000 genomes]
rs12124822	1.00[YRI][hapmap]
rs12125503	1.00[YRI][hapmap]
rs12128049	1.00[YRI][hapmap]
rs12132273	1.00[YRI][hapmap]
rs12135843	1.00[YRI][hapmap]
rs12140227	1.00[YRI][hapmap]
rs12141929	1.00[YRI][hapmap]
rs12565526	0.92[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1470898	0.87[ASN][1000 genomes]
rs17100509	1.00[ASW][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17100513	1.00[ASW][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17378915	1.00[ASW][hapmap]
rs2602936	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2602937	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2602945	1.00[ASW][hapmap]
rs2602948	1.00[ASW][hapmap]
rs2689676	1.00[ASW][hapmap]
rs2689683	1.00[ASW][hapmap]
rs2815307	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[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];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2815319	1.00[ASW][hapmap]
rs28701620	0.95[ASN][1000 genomes]
rs3862893	0.95[ASN][1000 genomes]
rs4949800	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs6704312	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7546116	0.91[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription 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
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS 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	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv2764210	chr1:77825478-77838400	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3438559	chr1:77832189-77834737	Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
9	esv3345903	chr1:77832439-77834787	Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77795000-77836400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:77803400-77839200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:77814400-77835600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:77819800-77835600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:77820400-77836400	Weak transcription	Primary T cells from cord blood	blood
6	chr1:77821000-77835600	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:77824400-77836400	Weak transcription	Brain Anterior Caudate	brain
8	chr1:77826200-77836400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:77830200-77835200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:77831600-77835600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr1:77831600-77835800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:77833200-77835800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:77834000-77839800	Enhancers	NHDF-Ad	bronchial
14	chr1:77834200-77834400	Enhancers	Brain Cingulate Gyrus	brain
15	chr1:77834200-77834600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr1:77834200-77834600	Enhancers	Brain Substantia Nigra	brain
17	chr1:77834200-77835600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:77834200-77835600	Enhancers	HSMM	muscle
19	chr1:77834200-77836400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:77834200-77836600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:77834200-77839000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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