Variant report

Variant	rs6804655
Chromosome Location	chr3:49738945-49738946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49737567..49739735-chr3:49821150..49823977,2	MCF-7	breast:
2	chr3:49735446..49741255-chr3:49749875..49755830,7	K562	blood:
3	chr3:49711656..49713849-chr3:49736490..49739042,2	MCF-7	breast:
4	chr3:49738438..49740011-chr3:49839951..49842563,2	K562	blood:
5	chr3:49724739..49727802-chr3:49735823..49739048,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185614	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000173531	Chromatin interaction
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10049413	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1049256	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs10865958	0.85[ASN][1000 genomes]
rs10865959	0.88[CHB][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130216	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];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs11130218	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130219	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130221	0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs1128535	0.85[ASN][1000 genomes]
rs11709680	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11710675	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714957	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11715304	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11716575	0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11717256	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11717463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11920900	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12381242	0.94[ASN][1000 genomes]
rs12490656	0.87[ASN][1000 genomes]
rs12496226	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13063621	0.92[ASN][1000 genomes]
rs13084243	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13085679	0.85[ASN][1000 genomes]
rs13086130	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13086465	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13090611	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1317140	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes]
rs13316065	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1491986	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs1799843	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1799845	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2234385	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2234391	0.96[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs2246832	0.82[ASN][1000 genomes]
rs2247036	0.82[ASN][1000 genomes]
rs2271960	0.96[CHD][hapmap];0.87[GIH][hapmap];0.82[ASN][1000 genomes]
rs2271961	0.96[CHD][hapmap];0.85[GIH][hapmap];0.82[ASN][1000 genomes]
rs2276864	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs2291542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2352967	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2352974	0.96[CHD][hapmap];0.91[GIH][hapmap];0.82[ASN][1000 genomes]
rs2352975	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34451146	0.92[ASN][1000 genomes]
rs34522271	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34614773	0.94[ASN][1000 genomes]
rs34735338	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35210174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35261599	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs35474403	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3749237	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3749240	1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs3749241	0.96[ASN][1000 genomes]
rs3811695	0.92[ASN][1000 genomes]
rs3811696	0.94[ASN][1000 genomes]
rs3819325	0.81[ASN][1000 genomes]
rs4768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4855841	0.91[ASN][1000 genomes]
rs4855850	0.92[ASN][1000 genomes]
rs4855862	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs4855867	0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs57648519	0.92[ASN][1000 genomes]
rs59906301	0.90[ASN][1000 genomes]
rs60205400	0.92[ASN][1000 genomes]
rs62260715	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260719	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62260729	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6446295	0.94[ASN][1000 genomes]
rs6766836	0.92[ASN][1000 genomes]
rs6775384	0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs6785549	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6802890	0.91[CHD][hapmap];0.91[GIH][hapmap];0.89[ASN][1000 genomes]
rs695238	0.96[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs71324996	0.83[EUR][1000 genomes]
rs7372725	0.88[ASN][1000 genomes]
rs7372730	0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7372966	0.95[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs7374183	0.95[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs7374277	0.88[ASN][1000 genomes]
rs7429353	0.88[ASN][1000 genomes]
rs7431078	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7431106	0.82[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.92[ASN][1000 genomes]
rs7618501	0.93[ASN][1000 genomes]
rs7618519	0.94[ASN][1000 genomes]
rs7629936	0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[YRI][hapmap];0.87[ASN][1000 genomes]
rs7634886	0.89[ASN][1000 genomes]
rs7634902	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs7645061	0.96[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs7648987	0.96[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs7649348	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs9814765	0.89[ASN][1000 genomes]
rs9815766	0.82[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs9819511	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9850465	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9853458	0.94[ASN][1000 genomes]
rs9855505	0.95[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs9859153	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9865480	0.94[ASN][1000 genomes]
rs9871654	0.91[ASN][1000 genomes]
rs9872864	0.95[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs9873183	0.94[ASN][1000 genomes]
rs9876508	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs9882639	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6804655	RBM6	cis	parietal	SCAN
rs6804655	AMT	cis	cerebellum	SCAN
rs6804655	WDR6	cis	Whole Blood	GTEx
rs6804655	C3orf54	cis	cerebellum	SCAN
rs6804655	ALS2CL	cis	cerebellum	SCAN
rs6804655	CCDC71	cis	cerebellum	SCAN
rs6804655	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs6804655	WDR6	cis	parietal	SCAN
rs6804655	UCN2	cis	cerebellum	SCAN
rs6804655	RBM6	cis	Nerve Tibial	GTEx
rs6804655	RNF123	cis	cerebellum	SCAN
rs6804655	P4HTM	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49727800-49740000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49727800-49742200	Weak transcription	Small Intestine	intestine
3	chr3:49728000-49739200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:49728000-49739200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:49728000-49739400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:49728000-49742600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:49728000-49744400	Weak transcription	NH-A	brain
8	chr3:49728000-49748800	Weak transcription	A549	lung
9	chr3:49728400-49753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:49728400-49756600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:49728600-49739400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:49728600-49744800	Weak transcription	HMEC	breast
13	chr3:49728600-49750400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:49729200-49749800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:49729200-49750200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:49729200-49755800	Weak transcription	Right Atrium	heart
17	chr3:49729400-49750200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:49731800-49740800	Strong transcription	Fetal Stomach	stomach
19	chr3:49732200-49755000	Strong transcription	Fetal Intestine Small	intestine
20	chr3:49732400-49739000	Enhancers	Fetal Heart	heart
21	chr3:49733000-49750200	Weak transcription	Psoas Muscle	Psoas
22	chr3:49734200-49746000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:49734200-49746000	Strong transcription	Thymus	Thymus
24	chr3:49734200-49746200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr3:49734400-49740400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:49734400-49740600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:49734400-49740800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr3:49734400-49741200	Strong transcription	Spleen	Spleen
29	chr3:49734400-49744000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:49734400-49744000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:49734400-49744200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:49734400-49744400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:49734400-49744800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:49734400-49744800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr3:49734400-49745000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:49734400-49745200	Strong transcription	Fetal Brain Female	brain
37	chr3:49734400-49745400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr3:49734400-49745400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:49734400-49746000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:49734400-49746000	Strong transcription	Fetal Intestine Large	intestine
41	chr3:49734400-49746200	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr3:49734400-49746200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr3:49734400-49746200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:49734400-49746400	Strong transcription	Brain Hippocampus Middle	brain
45	chr3:49734400-49756000	Strong transcription	Liver	Liver
46	chr3:49734600-49739400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
47	chr3:49734600-49740400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:49734600-49740600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:49734600-49741000	Strong transcription	Brain Angular Gyrus	brain
50	chr3:49734600-49741000	Strong transcription	Lung	lung

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