Variant report

Variant	rs6485690
Chromosome Location	chr11:46798631-46798632
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	chr11:46798348..46800815-chr11:46802877..46805320,2	MCF-7	breast:
2	chr11:46785236..46787820-chr11:46798096..46801052,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1007738	0.91[GIH][hapmap]
rs10734548	0.94[GIH][hapmap]
rs10769205	0.83[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs10769211	0.91[GIH][hapmap]
rs10838621	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838622	0.80[AMR][1000 genomes]
rs11039014	0.91[GIH][hapmap]
rs12361673	0.83[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs13448	0.89[GIH][hapmap]
rs1551744	0.91[GIH][hapmap]
rs2070852	0.91[ASW][hapmap];0.83[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs2306029	0.81[ASW][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2306032	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4606447	0.89[GIH][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs6485696	0.81[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6485702	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7101374	0.91[GIH][hapmap]
rs7107778	0.94[GIH][hapmap]
rs7929294	0.94[GIH][hapmap]
rs7932354	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7940441	0.83[GIH][hapmap];0.80[MEX][hapmap]
rs964551	0.94[GIH][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	nsv430382	chr11:46743135-46849360	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv3388509	chr11:46763105-46818814	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6485690	ARHGAP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46761400-46840000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:46761400-46845200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:46761600-46824600	Strong transcription	Fetal Thymus	thymus
4	chr11:46762600-46804000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:46762600-46826000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:46762600-46841400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:46762800-46804800	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:46762800-46835600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr11:46762800-46842400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr11:46763400-46839600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:46770200-46818200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:46778800-46841200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:46779400-46824600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:46780600-46814000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr11:46782600-46847400	Weak transcription	Stomach Mucosa	stomach
16	chr11:46784000-46804000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr11:46784200-46800000	Weak transcription	Gastric	stomach
18	chr11:46784400-46800800	Weak transcription	Esophagus	oesophagus
19	chr11:46785800-46807800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:46786000-46799000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:46786000-46809600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:46787000-46828200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr11:46787800-46824600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:46788000-46826200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:46788200-46825800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr11:46788200-46841400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:46788600-46824200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr11:46788600-46840600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr11:46788800-46824000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:46791800-46799000	Weak transcription	Right Ventricle	heart
31	chr11:46791800-46800000	Weak transcription	Aorta	Aorta
32	chr11:46791800-46801400	Weak transcription	Psoas Muscle	Psoas
33	chr11:46792000-46799600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:46792000-46799600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr11:46792000-46803200	Weak transcription	Fetal Heart	heart
36	chr11:46792000-46805800	Weak transcription	Small Intestine	intestine
37	chr11:46792600-46799000	Weak transcription	Colonic Mucosa	Colon
38	chr11:46792600-46799000	Weak transcription	Lung	lung
39	chr11:46792600-46799000	Weak transcription	Pancreas	Pancrea
40	chr11:46792600-46799000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr11:46792600-46799000	Weak transcription	Spleen	Spleen
42	chr11:46792600-46800000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:46793000-46799000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr11:46793000-46799000	Weak transcription	HSMMtube	muscle
45	chr11:46793200-46799000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr11:46795200-46820400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:46795400-46800000	Weak transcription	Fetal Intestine Small	intestine
48	chr11:46795600-46800000	Weak transcription	Fetal Stomach	stomach
49	chr11:46796200-46807400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:46796400-46821400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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