Variant report

Variant	rs10895009
Chromosome Location	chr11:100585889-100585890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:100578654..100584539-chr11:100585758..100591241,5	K562	blood:
2	chr11:100582193..100584902-chr11:100585301..100588022,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10128687	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10431108	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895001	0.81[CHD][hapmap]
rs10895011	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11224403	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11224417	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1216743	0.88[ASN][1000 genomes]
rs12269905	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12286062	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12288075	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12291493	0.92[ASN][1000 genomes]
rs1502284	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1532710	0.81[CHD][hapmap]
rs1847149	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1847150	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2055449	0.83[ASN][1000 genomes]
rs2055450	0.84[ASN][1000 genomes]
rs2298609	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4312035	0.86[CHB][hapmap];0.95[CHD][hapmap];0.84[ASN][1000 genomes]
rs4495864	0.87[ASN][1000 genomes]
rs4753980	0.81[ASN][1000 genomes]
rs4753984	0.94[ASN][1000 genomes]
rs4754695	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4754697	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4754698	0.88[ASN][1000 genomes]
rs486023	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs492237	0.91[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs604723	0.93[ASN][1000 genomes]
rs607562	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs633185	0.94[ASN][1000 genomes]
rs653320	0.88[ASN][1000 genomes]
rs6590805	0.80[ASN][1000 genomes]
rs6590810	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6590811	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6590812	0.95[ASN][1000 genomes]
rs6590813	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6590814	0.97[ASN][1000 genomes]
rs6590816	0.83[ASN][1000 genomes]
rs6590817	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs667575	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs670401	0.88[ASN][1000 genomes]
rs7103397	0.94[ASN][1000 genomes]
rs7105451	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7106603	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7112041	0.94[ASN][1000 genomes]
rs7114867	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7125452	0.88[ASN][1000 genomes]
rs7130275	0.94[ASN][1000 genomes]
rs7926526	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7928576	0.93[ASN][1000 genomes]
rs7928871	0.85[ASN][1000 genomes]
rs7930157	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7938194	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7938601	0.85[ASN][1000 genomes]
rs7942556	0.81[CHD][hapmap]
rs7946913	0.80[AFR][1000 genomes]
rs7952055	0.93[ASN][1000 genomes]
rs9919648	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053430	chr11:99888390-100629136	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1042067	chr11:99889697-100629136	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv556122	chr11:99893282-100585889	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1037689	chr11:99895378-100624599	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1040942	chr11:99895378-100629136	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1039852	chr11:99901695-100610533	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv541152	chr11:99901695-100610533	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1045190	chr11:99913193-100627395	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv541153	chr11:99913193-100627395	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv529454	chr11:99913394-100627255	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1043022	chr11:100387466-100610533	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv832246	chr11:100426725-100606957	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv898327	chr11:100569021-100631075	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10895009	ARHGAP42	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100561000-100590200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr11:100561000-100590600	Weak transcription	Lung	lung
3	chr11:100564400-100586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:100566800-100590000	Weak transcription	Fetal Stomach	stomach
5	chr11:100572400-100590000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:100572400-100590200	Weak transcription	Placenta	Placenta
7	chr11:100575200-100590000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:100575400-100586200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr11:100575400-100587200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:100575400-100590200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:100575600-100586000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:100576200-100590200	Weak transcription	Small Intestine	intestine
13	chr11:100576800-100587600	Weak transcription	Primary B cells from cord blood	blood
14	chr11:100580200-100590200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr11:100580600-100586000	Weak transcription	A549	lung
16	chr11:100580800-100586000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:100580800-100586000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:100580800-100586000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr11:100580800-100586200	Weak transcription	Psoas Muscle	Psoas
20	chr11:100580800-100589800	Weak transcription	Fetal Heart	heart
21	chr11:100581000-100586000	Weak transcription	GM12878-XiMat	blood
22	chr11:100581000-100589800	Weak transcription	HSMMtube	muscle
23	chr11:100581000-100590000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:100581200-100586000	Weak transcription	Fetal Muscle Leg	muscle
25	chr11:100583600-100590000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:100583800-100589800	Weak transcription	Liver	Liver
27	chr11:100584200-100589000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr11:100584200-100590000	Weak transcription	Fetal Intestine Small	intestine
29	chr11:100584200-100590200	Weak transcription	Fetal Intestine Large	intestine
30	chr11:100584600-100586200	Weak transcription	Fetal Kidney	kidney
31	chr11:100584600-100588800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr11:100585000-100586200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr11:100585200-100587000	Enhancers	H9 Cell Line	embryonic stem cell
34	chr11:100585400-100586800	Enhancers	Left Ventricle	heart
35	chr11:100585400-100586800	Enhancers	Spleen	Spleen
36	chr11:100585400-100590200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr11:100585600-100586200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr11:100585600-100586400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr11:100585600-100586400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr11:100585600-100586400	Enhancers	Right Atrium	heart
41	chr11:100585600-100587000	Enhancers	NHLF	lung
42	chr11:100585600-100589800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:100585800-100586200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr11:100585800-100586200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:100585800-100586400	Enhancers	HUVEC	blood vessel
46	chr11:100585800-100586800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:100585800-100587000	Enhancers	Adipose Nuclei	Adipose
48	chr11:100585800-100588000	Enhancers	NHDF-Ad	bronchial
49	chr11:100585800-100590200	Weak transcription	Right Ventricle	heart

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