Variant report

Variant	rs6771713
Chromosome Location	chr3:136450593-136450594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136049332..136050837-chr3:136449297..136451050,2	MCF-7	breast:
2	chr3:136449340..136450986-chr3:136460962..136462477,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10155016	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10155017	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10513014	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12107125	0.92[AFR][1000 genomes]
rs12635723	0.85[LWK][hapmap];0.92[YRI][hapmap]
rs13433980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1484250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs1872240	0.98[EUR][1000 genomes]
rs28682370	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34992220	0.86[CEU][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs3932048	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs4336059	0.83[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap]
rs4678438	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs59931907	0.81[AFR][1000 genomes]
rs6439655	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs6763239	0.84[EUR][1000 genomes]
rs6765239	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs6772759	0.84[EUR][1000 genomes]
rs6782151	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs6789329	0.91[CEU][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6799699	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800969	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs73230077	0.81[ASN][1000 genomes]
rs73230078	0.81[ASN][1000 genomes]
rs7612160	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap]
rs7623824	0.94[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap]
rs7626418	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7629905	0.83[EUR][1000 genomes]
rs7644346	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7644471	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap]
rs9813596	0.82[AFR][1000 genomes]
rs9818372	0.83[EUR][1000 genomes]
rs9820513	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs9828068	0.83[EUR][1000 genomes]
rs9839574	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs9845762	0.85[LWK][hapmap];0.92[YRI][hapmap]
rs9845950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9853960	0.83[EUR][1000 genomes]
rs9869361	0.83[EUR][1000 genomes]
rs9869957	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9881078	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6771713	RNF184	cis	multi-tissue	Pritchard
rs6771713	SCN9A	trans	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136426600-136453400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:136427800-136452400	Weak transcription	HUVEC	blood vessel
3	chr3:136431000-136454600	Weak transcription	Hela-S3	cervix
4	chr3:136432400-136468200	Weak transcription	Aorta	Aorta
5	chr3:136432600-136454000	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:136433200-136462600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:136438000-136458000	Weak transcription	Esophagus	oesophagus
8	chr3:136438800-136461200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:136439200-136454400	Weak transcription	Fetal Stomach	stomach
10	chr3:136443600-136451400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:136443800-136452600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:136444000-136455000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr3:136444200-136455000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:136444400-136451000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr3:136444400-136451800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr3:136444600-136451200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:136444800-136450600	Enhancers	Small Intestine	intestine
18	chr3:136445200-136453400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:136445400-136460000	Weak transcription	Gastric	stomach
20	chr3:136446400-136453600	Weak transcription	Fetal Heart	heart
21	chr3:136446400-136460000	Weak transcription	K562	blood
22	chr3:136446600-136451800	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr3:136447800-136450800	Enhancers	Primary B cells from peripheral blood	blood
24	chr3:136447800-136451200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:136447800-136451600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr3:136448000-136453000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:136448000-136453200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:136448000-136453800	Weak transcription	Ovary	ovary
29	chr3:136448000-136455600	Weak transcription	Fetal Lung	lung
30	chr3:136448000-136460800	Weak transcription	Brain Germinal Matrix	brain
31	chr3:136448200-136450800	Enhancers	Brain Anterior Caudate	brain
32	chr3:136448200-136453200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:136448200-136453200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:136448200-136453400	Weak transcription	Adipose Nuclei	Adipose
35	chr3:136448200-136453600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:136448200-136453800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:136448200-136454000	Enhancers	Brain Substantia Nigra	brain
38	chr3:136448200-136455000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:136448200-136459800	Weak transcription	Osteobl	bone
40	chr3:136448200-136460000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:136448200-136467600	Weak transcription	HSMM	muscle
42	chr3:136448200-136467800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:136448200-136467800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:136448200-136467800	Weak transcription	HSMMtube	muscle
45	chr3:136448400-136453200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:136448400-136455400	Weak transcription	NH-A	brain
47	chr3:136448400-136459800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:136448600-136460200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:136448600-136462800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:136448600-136463800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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