Variant report

Variant	rs3779200
Chromosome Location	chr7:39737269-39737270
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	chr7:39736311-39737300	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr7:39736792-39737897	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39736933..39739214-chr7:39753535..39757472,3	K562	blood:

Variant related genes	Relation type
RALA	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10253933	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10267545	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10486803	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10486805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs11765970	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11773499	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs11773617	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12668144	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12669963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs12701754	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12701755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs12701756	0.83[ASN][1000 genomes]
rs12701757	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.83[ASN][1000 genomes]
rs12701759	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13244194	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13247563	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17417049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs17417084	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34063025	1.00[ASN][1000 genomes]
rs34910913	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35314132	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35774126	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62453003	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6462940	1.00[ASN][1000 genomes]
rs6968684	1.00[ASN][1000 genomes]
rs6976944	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6977082	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7778955	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[ASN][1000 genomes]
rs7779169	0.83[ASN][1000 genomes]
rs7782931	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7792940	1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs7797693	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9648483	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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3779200	C7orf11	cis	cerebellum	SCAN

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	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
3	chr7:39718200-39739800	Weak transcription	Spleen	Spleen
4	chr7:39721200-39738200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:39722000-39737600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:39722800-39738400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:39723600-39742800	Weak transcription	Brain Angular Gyrus	brain
8	chr7:39723800-39743000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:39724000-39739400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:39724200-39741200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:39724600-39739000	Weak transcription	Small Intestine	intestine
12	chr7:39726600-39742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:39727000-39738000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:39727400-39741600	Strong transcription	Fetal Muscle Leg	muscle
15	chr7:39727400-39747800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:39727600-39741200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr7:39728800-39739800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:39729000-39739400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:39729000-39742400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr7:39729400-39739000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:39729400-39740000	Weak transcription	Stomach Mucosa	stomach
22	chr7:39730000-39741600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr7:39730600-39737600	Weak transcription	Fetal Brain Male	brain
24	chr7:39730600-39749200	Weak transcription	Ovary	ovary
25	chr7:39731400-39740800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr7:39732000-39738000	Weak transcription	Hela-S3	cervix
27	chr7:39732000-39739200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:39732000-39748000	Strong transcription	HUVEC	blood vessel
29	chr7:39732000-39749200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:39732800-39741000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:39733000-39741600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:39733800-39739200	Weak transcription	Brain Germinal Matrix	brain
33	chr7:39734200-39738600	Strong transcription	NHEK	skin
34	chr7:39734200-39739200	Weak transcription	Brain Substantia Nigra	brain
35	chr7:39734200-39746200	Weak transcription	Fetal Kidney	kidney
36	chr7:39734600-39743000	Strong transcription	HSMM	muscle
37	chr7:39735200-39737800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:39735200-39738000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr7:39735200-39738800	Strong transcription	Fetal Lung	lung
40	chr7:39735200-39739000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:39735200-39740400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr7:39735200-39741400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr7:39735400-39739000	Strong transcription	HMEC	breast
44	chr7:39735400-39739400	Weak transcription	Fetal Intestine Small	intestine
45	chr7:39735400-39740200	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr7:39735400-39740600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr7:39735600-39737400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:39735600-39737400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr7:39735600-39737600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:39735600-39737600	Genic enhancers	NHDF-Ad	bronchial

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