Variant report

Variant	rs4713857
Chromosome Location	chr6:11761459-11761460
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11760325..11763713-chr6:11770760..11773174,3	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1413345	0.89[JPT][hapmap]
rs2235427	0.89[JPT][hapmap]
rs4140558	0.82[MKK][hapmap];0.80[YRI][hapmap]
rs4713856	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713873	0.81[CHB][hapmap]
rs9348976	0.88[ASW][hapmap];0.95[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4713857	C6orf52	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11719400-11762200	Weak transcription	Colonic Mucosa	Colon
2	chr6:11738600-11762000	Weak transcription	Gastric	stomach
3	chr6:11753200-11763800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:11755800-11768400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:11758600-11762000	Weak transcription	HMEC	breast
6	chr6:11758600-11762400	Weak transcription	Spleen	Spleen
7	chr6:11759000-11765800	Enhancers	Fetal Intestine Large	intestine
8	chr6:11759200-11764400	Enhancers	Stomach Mucosa	stomach
9	chr6:11759200-11765600	Enhancers	Fetal Intestine Small	intestine
10	chr6:11759400-11763600	Weak transcription	Esophagus	oesophagus
11	chr6:11759400-11769600	Weak transcription	Lung	lung
12	chr6:11759600-11762000	Weak transcription	NHEK	skin
13	chr6:11759600-11762200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:11759600-11762600	Weak transcription	A549	lung
15	chr6:11759600-11763400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:11759600-11765000	Enhancers	Duodenum Mucosa	Duodenum
17	chr6:11759600-11765800	Weak transcription	Hela-S3	cervix
18	chr6:11759800-11762000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:11759800-11764400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr6:11760000-11761600	Enhancers	K562	blood
21	chr6:11760000-11761800	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr6:11760000-11763400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:11760400-11762000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:11760400-11762400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:11760400-11765800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:11760600-11762400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:11760600-11762800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:11760600-11763600	Weak transcription	Ovary	ovary
29	chr6:11760600-11763600	Weak transcription	Right Atrium	heart
30	chr6:11760600-11766000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:11760600-11770600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:11760800-11763600	Weak transcription	Small Intestine	intestine
33	chr6:11761000-11762000	Weak transcription	Pancreas	Pancrea
34	chr6:11761000-11762600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:11761000-11763200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:11761400-11762800	Enhancers	Rectal Mucosa Donor 29	rectum

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