Variant report

Variant	rs10947946
Chromosome Location	chr6:12327232-12327233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:12326975..12328515-chr6:12341248..12343129,2	MCF-7	breast:
2	chr6:12318347..12320917-chr6:12327071..12328743,2	MCF-7	breast:
3	chr6:12327141..12329484-chr6:12596719..12598880,2	MCF-7	breast:
4	chr6:12322236..12325054-chr6:12326610..12329434,2	K562	blood:
5	chr6:12286691..12293887-chr6:12327157..12336724,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000218893	Chromatin interaction
ENSG00000078401	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10947935	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11752276	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11755836	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11757019	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12530046	0.83[ASN][1000 genomes]
rs16872608	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17765653	0.83[CHB][hapmap]
rs2032549	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4711654	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4714414	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4714419	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4714429	1.00[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs62389535	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62389538	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357344	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369245	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9369246	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9381013	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9381033	0.87[CHB][hapmap];0.91[JPT][hapmap]

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	nsv508394	chr6:12285464-12386745	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10947946	RNF182	cis	parietal	SCAN
rs10947946	EDN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12315200-12327800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:12323800-12328000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr6:12324400-12327400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:12324400-12328600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:12324400-12329200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr6:12324600-12328600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:12324800-12328800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:12324800-12328800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:12324800-12328800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:12324800-12331000	Weak transcription	Pancreas	Pancrea
11	chr6:12325000-12327800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:12325200-12327600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:12325200-12328600	Enhancers	NHEK	skin
14	chr6:12325200-12331600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:12325200-12332200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:12325400-12327800	Weak transcription	HepG2	liver
17	chr6:12325400-12328800	Weak transcription	Fetal Intestine Small	intestine
18	chr6:12325400-12328800	Weak transcription	Stomach Mucosa	stomach
19	chr6:12325400-12329000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:12325400-12329600	Enhancers	A549	lung
21	chr6:12325400-12331000	Weak transcription	Fetal Intestine Large	intestine
22	chr6:12325400-12332000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:12325800-12327800	Weak transcription	Hela-S3	cervix
24	chr6:12325800-12328600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:12325800-12328600	Weak transcription	Fetal Thymus	thymus
26	chr6:12326200-12327600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:12326200-12329400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr6:12326600-12328000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr6:12326600-12329000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr6:12326600-12329200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr6:12327000-12327400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:12327000-12327400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:12327000-12328200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:12327000-12329600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:12327000-12330200	Enhancers	HMEC	breast
36	chr6:12327200-12328800	Weak transcription	H9 Cell Line	embryonic stem cell

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