Variant report

Variant	rs3779203
Chromosome Location	chr7:39736796-39736797
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	chr7:39736791-39736806	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr7:39736311-39737300	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr7:39736792-39737897	K562	blood:	n/a	n/a

Variant related genes	Relation type
RALA	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10231409	0.90[JPT][hapmap]
rs10486799	1.00[GIH][hapmap];1.00[AFR][1000 genomes]
rs10486802	0.89[JPT][hapmap]
rs17171616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17416875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17507811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17508730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17509194	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17714061	0.82[GIH][hapmap];1.00[AFR][1000 genomes]
rs3801265	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56719666	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73377485	0.87[EUR][1000 genomes]
rs73381122	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73381129	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73387354	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7796021	0.90[JPT][hapmap]
rs7799721	0.89[JPT][hapmap]

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	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39701800-39739400	Weak transcription	Esophagus	oesophagus
2	chr7:39714000-39736800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
4	chr7:39718200-39739800	Weak transcription	Spleen	Spleen
5	chr7:39721200-39738200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr7:39722000-39737600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr7:39722800-39738400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:39723400-39736800	Weak transcription	Brain Hippocampus Middle	brain
9	chr7:39723600-39742800	Weak transcription	Brain Angular Gyrus	brain
10	chr7:39723800-39737000	Weak transcription	Brain Anterior Caudate	brain
11	chr7:39723800-39743000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:39724000-39739400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:39724200-39741200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:39724600-39739000	Weak transcription	Small Intestine	intestine
15	chr7:39726400-39736800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:39726400-39737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:39726600-39742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr7:39727000-39738000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:39727400-39741600	Strong transcription	Fetal Muscle Leg	muscle
20	chr7:39727400-39747800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:39727600-39741200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr7:39728800-39736800	Weak transcription	Gastric	stomach
23	chr7:39728800-39736800	Weak transcription	Lung	lung
24	chr7:39728800-39737000	Weak transcription	Right Ventricle	heart
25	chr7:39728800-39739800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr7:39729000-39739400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:39729000-39742400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr7:39729400-39739000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:39729400-39740000	Weak transcription	Stomach Mucosa	stomach
30	chr7:39729600-39736800	Weak transcription	Pancreas	Pancrea
31	chr7:39730000-39741600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr7:39730600-39736800	Weak transcription	Left Ventricle	heart
33	chr7:39730600-39737000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr7:39730600-39737200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr7:39730600-39737600	Weak transcription	Fetal Brain Male	brain
36	chr7:39730600-39749200	Weak transcription	Ovary	ovary
37	chr7:39731400-39740800	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr7:39732000-39736800	Weak transcription	Fetal Brain Female	brain
39	chr7:39732000-39738000	Weak transcription	Hela-S3	cervix
40	chr7:39732000-39739200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:39732000-39748000	Strong transcription	HUVEC	blood vessel
42	chr7:39732000-39749200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:39732800-39741000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:39733000-39741600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr7:39733800-39739200	Weak transcription	Brain Germinal Matrix	brain
46	chr7:39734200-39738600	Strong transcription	NHEK	skin
47	chr7:39734200-39739200	Weak transcription	Brain Substantia Nigra	brain
48	chr7:39734200-39746200	Weak transcription	Fetal Kidney	kidney
49	chr7:39734600-39743000	Strong transcription	HSMM	muscle
50	chr7:39735200-39737000	Strong transcription	Osteobl	bone

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