Variant report

Variant	rs3779500
Chromosome Location	chr7:106792704-106792705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:106790717..106794481-chr7:106808251..106810689,4	MCF-7	breast:
2	chr7:106791621..106793929-chr7:107384151..107385993,2	K562	blood:
3	chr7:106785772..106788697-chr7:106791053..106792877,2	K562	blood:
4	chr7:106591017..106592710-chr7:106791825..106794582,2	K562	blood:
5	chr7:106646754..106649589-chr7:106791342..106793734,2	K562	blood:
6	chr7:106791219..106793947-chr7:106800933..106803916,2	K562	blood:
7	chr7:106586596..106588761-chr7:106790457..106792904,2	K562	blood:
8	chr7:106787472..106790452-chr7:106792123..106795407,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105856	Chromatin interaction
ENSG00000241764	Chromatin interaction
ENSG00000105879	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1002935	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs1018946	0.84[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes]
rs1018947	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs10253172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261881	0.81[ASN][1000 genomes]
rs10272371	1.00[CHD][hapmap]
rs10487271	0.84[CEU][hapmap]
rs10953529	0.83[AMR][1000 genomes]
rs10953530	0.84[CEU][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes]
rs10953531	0.84[CEU][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes]
rs11509187	0.81[ASN][1000 genomes]
rs11767623	0.93[CEU][hapmap];1.00[CHB][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]
rs12055946	0.81[ASN][1000 genomes]
rs12532447	0.89[CEU][hapmap]
rs12532849	0.84[CEU][hapmap]
rs12532953	0.89[AMR][1000 genomes]
rs12533767	0.89[AMR][1000 genomes]
rs12535258	0.84[CEU][hapmap]
rs12536574	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12537374	0.80[AMR][1000 genomes]
rs12537730	0.89[AMR][1000 genomes]
rs12540475	0.80[AMR][1000 genomes]
rs12705405	1.00[CEU][hapmap];1.00[CHB][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]
rs17153823	1.00[CHD][hapmap]
rs17153861	0.81[ASN][1000 genomes]
rs17341680	0.81[ASN][1000 genomes]
rs17349904	0.84[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes]
rs17425839	1.00[CHD][hapmap]
rs17427123	0.89[AMR][1000 genomes]
rs17427158	0.89[AMR][1000 genomes]
rs17427849	0.89[AMR][1000 genomes]
rs17428071	0.84[CEU][hapmap];0.80[AMR][1000 genomes]
rs17428126	0.80[AMR][1000 genomes]
rs1981696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023892	0.89[AMR][1000 genomes]
rs2107318	0.89[AMR][1000 genomes]
rs2107319	0.84[CEU][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs2191917	0.81[ASN][1000 genomes]
rs2249043	0.84[CEU][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]
rs2250121	1.00[CHD][hapmap]
rs257371	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257372	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257373	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257375	1.00[ASW][hapmap];0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257379	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257381	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257382	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257385	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257386	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28610544	0.81[ASN][1000 genomes]
rs2894459	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs3729876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729877	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752645	1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs3801963	0.83[CEU][hapmap]
rs3801965	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs4727671	0.80[AMR][1000 genomes]
rs4730222	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4730223	0.84[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4730224	0.89[AMR][1000 genomes]
rs4730226	0.80[AMR][1000 genomes]
rs61014091	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61673847	0.80[AMR][1000 genomes]
rs6466160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946036	0.89[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes]
rs6946931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947675	0.82[CEU][hapmap];0.89[AMR][1000 genomes]
rs6947857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949961	0.84[CEU][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes]
rs6951639	0.89[AMR][1000 genomes]
rs6960148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6960708	1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs6967745	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs6971393	0.81[ASN][1000 genomes]
rs6971675	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs6971774	0.84[CEU][hapmap];0.92[GIH][hapmap];0.87[AMR][1000 genomes]
rs6977868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978486	0.81[ASN][1000 genomes]
rs7777976	0.80[AMR][1000 genomes]
rs7781947	0.84[CEU][hapmap]
rs7786692	1.00[CHD][hapmap]
rs7789678	0.82[AMR][1000 genomes]
rs7793594	0.80[AMR][1000 genomes]
rs7794598	0.84[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs7794915	0.85[GIH][hapmap];0.93[MEX][hapmap]
rs7794965	0.82[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes]
rs7798223	0.89[AMR][1000 genomes]
rs7981	0.81[CEU][hapmap];0.89[AMR][1000 genomes]
rs8180787	0.81[ASN][1000 genomes]
rs9641378	0.84[CEU][hapmap];0.83[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831087	chr7:106673465-106872460	Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3779500	NFIL3	trans	lymphoblastoid	seeQTL
rs3779500	NRCAM	cis	parietal	SCAN
rs3779500	BCAP29	cis	parietal	SCAN
rs3779500	GPR22	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106760400-106808400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:106763000-106807800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:106767400-106797600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr7:106778400-106807800	Weak transcription	Brain Germinal Matrix	brain
5	chr7:106780000-106807800	Weak transcription	Fetal Heart	heart
6	chr7:106782000-106795400	Weak transcription	Pancreas	Pancrea
7	chr7:106782600-106808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:106782800-106807800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:106783600-106807600	Weak transcription	Fetal Stomach	stomach
10	chr7:106784200-106802600	Strong transcription	K562	blood
11	chr7:106785400-106808000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:106785800-106807600	Weak transcription	Fetal Kidney	kidney
13	chr7:106787400-106805800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:106788000-106805800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:106788000-106808000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr7:106788200-106807600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr7:106788400-106794000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:106788400-106808000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:106788600-106805800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:106788800-106797200	Weak transcription	Placenta	Placenta
21	chr7:106788800-106797400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:106788800-106805800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:106788800-106807200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:106788800-106807600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr7:106788800-106807800	Weak transcription	Ovary	ovary
26	chr7:106789400-106808200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:106790000-106807200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:106790800-106797800	Weak transcription	Spleen	Spleen
29	chr7:106791000-106799400	Weak transcription	HUVEC	blood vessel
30	chr7:106791000-106805600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:106791000-106806800	Weak transcription	Fetal Intestine Large	intestine
32	chr7:106791000-106807600	Weak transcription	Brain Anterior Caudate	brain
33	chr7:106791200-106795200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr7:106791200-106799400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr7:106791200-106807800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:106791800-106792800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:106791800-106793000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:106791800-106793000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr7:106791800-106794400	Strong transcription	Adipose Nuclei	Adipose
40	chr7:106792000-106792800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:106792000-106792800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:106792000-106792800	Enhancers	NH-A	brain
43	chr7:106792000-106792800	Enhancers	NHDF-Ad	bronchial
44	chr7:106792000-106792800	Enhancers	NHLF	lung
45	chr7:106792000-106793000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr7:106792000-106793000	Enhancers	HMEC	breast
47	chr7:106792200-106793000	Strong transcription	Fetal Brain Female	brain
48	chr7:106792200-106808400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr7:106792400-106792800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:106792600-106793000	Enhancers	Hela-S3	cervix

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