Variant report

Variant	rs9470702
Chromosome Location	chr6:37756100-37756101
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37741856..37743598-chr6:37754566..37756274,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10456096	0.85[CEU][hapmap]
rs10485029	0.82[CHD][hapmap]
rs12200258	0.88[CEU][hapmap]
rs12211981	0.92[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs12213835	0.92[CEU][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap]
rs13210701	0.92[CEU][hapmap]
rs2055206	0.84[CEU][hapmap]
rs259686	0.88[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs259689	0.92[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs259690	0.92[CEU][hapmap]
rs259691	0.92[CEU][hapmap]
rs259713	0.92[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs2645107	0.88[CEU][hapmap]
rs2645116	0.88[CEU][hapmap]
rs2842517	0.88[CEU][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap]
rs4714105	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6458029	0.92[CEU][hapmap]
rs6941057	0.81[CEU][hapmap]
rs9296232	0.92[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap]
rs9394460	0.92[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs9470701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9470702	KCNK17	cis	parietal	SCAN
rs9470702	TAF11	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37752600-37758000	Weak transcription	Liver	Liver
2	chr6:37752600-37758600	Weak transcription	Fetal Brain Female	brain
3	chr6:37752600-37758800	Weak transcription	HSMMtube	muscle
4	chr6:37753000-37758400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:37753200-37758000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:37753200-37758200	Weak transcription	Ovary	ovary
7	chr6:37753200-37758800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:37753200-37759000	Weak transcription	Right Atrium	heart
9	chr6:37753400-37758200	Weak transcription	Pancreas	Pancrea
10	chr6:37753400-37758800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:37753400-37758800	Weak transcription	Esophagus	oesophagus
12	chr6:37753600-37758000	Weak transcription	Fetal Brain Male	brain
13	chr6:37753800-37758800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:37753800-37758800	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:37754000-37758600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:37754000-37758800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:37755000-37758800	Weak transcription	Fetal Intestine Small	intestine
18	chr6:37755200-37759000	Weak transcription	Fetal Intestine Large	intestine
19	chr6:37755400-37756400	Enhancers	Placenta	Placenta
20	chr6:37755400-37756400	Enhancers	NHDF-Ad	bronchial
21	chr6:37755400-37759000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:37755600-37756200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:37755600-37756600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:37755600-37756600	Enhancers	HMEC	breast
25	chr6:37755600-37756600	Enhancers	NHEK	skin
26	chr6:37755600-37756800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:37755800-37756400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:37755800-37756400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:37755800-37756400	Enhancers	A549	lung
30	chr6:37755800-37756400	Enhancers	NHLF	lung
31	chr6:37755800-37756600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:37755800-37756800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:37755800-37758400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:37755800-37758600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:37755800-37758600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:37756000-37756200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr6:37756000-37756200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr6:37756000-37756600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:37756000-37756600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:37756000-37756600	Enhancers	HSMM	muscle
41	chr6:37756000-37758600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr6:37756000-37758800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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