Variant report

Variant	rs9462681
Chromosome Location	chr6:12342421-12342422
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:12341393..12343735-chr6:12346097..12348684,2	MCF-7	breast:
2	chr6:12326975..12328515-chr6:12341248..12343129,2	MCF-7	breast:
3	chr6:12341804..12346306-chr6:12347487..12351106,5	MCF-7	breast:
4	chr6:12329368..12332356-chr6:12340558..12342942,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10807258	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947949	0.82[EUR][1000 genomes]
rs2095344	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2095345	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2184329	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2327544	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6932390	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9357346	0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs9369262	0.80[JPT][hapmap];0.80[EUR][1000 genomes]
rs9462684	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9471538	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]

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	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
2	nsv528681	chr6:12340034-12362219	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12332200-12344000	Weak transcription	Aorta	Aorta
2	chr6:12336000-12343400	Weak transcription	Fetal Kidney	kidney
3	chr6:12337200-12348600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:12338200-12343000	Enhancers	Liver	Liver
5	chr6:12338200-12345800	Enhancers	Fetal Intestine Small	intestine
6	chr6:12338600-12342600	Enhancers	A549	lung
7	chr6:12338800-12345800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr6:12339000-12346200	Enhancers	Fetal Intestine Large	intestine
9	chr6:12340800-12343200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:12340800-12343600	Enhancers	HepG2	liver
11	chr6:12340800-12344000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:12340800-12348000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:12341000-12343400	Weak transcription	NHEK	skin
14	chr6:12341000-12348000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:12341400-12342800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr6:12341400-12343000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:12341400-12344000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:12341600-12342600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:12341600-12342600	Enhancers	Gastric	stomach
20	chr6:12341600-12343800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr6:12341600-12344800	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr6:12341600-12345800	Enhancers	Duodenum Mucosa	Duodenum
23	chr6:12341600-12346800	Enhancers	Stomach Mucosa	stomach
24	chr6:12341800-12342600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:12341800-12343000	Enhancers	H1 Cell Line	embryonic stem cell
26	chr6:12341800-12343200	Enhancers	Colonic Mucosa	Colon
27	chr6:12341800-12343800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr6:12341800-12344400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:12342000-12342600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:12342000-12342600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:12342000-12342800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr6:12342000-12342800	Enhancers	Small Intestine	intestine
33	chr6:12342000-12343200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:12342000-12343200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:12342000-12344200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:12342000-12344200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr6:12342000-12344400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr6:12342000-12344600	Enhancers	Hela-S3	cervix
39	chr6:12342000-12347000	Enhancers	Pancreas	Pancrea
40	chr6:12342200-12343600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:12342400-12342800	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr6:12342400-12342800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr6:12342400-12343200	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr6:12342400-12344200	Enhancers	Muscle Satellite Cultured Cells	--

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