Variant report

Variant	rs9461230
Chromosome Location	chr6:26019240-26019241
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26017750..26036418-chr6:26116875..26130553,65	MCF-7	breast:
2	chr6:26018945..26024445-chr6:27858774..27864727,7	MCF-7	breast:
3	chr6:26016695..26019436-chr6:26198057..26199976,2	MCF-7	breast:
4	chr6:26019231..26022068-chr6:26204049..26206272,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180596	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000180573	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10807006	0.86[AMR][1000 genomes]
rs10807007	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10946800	0.82[ASN][1000 genomes]
rs1115920	0.82[ASN][1000 genomes]
rs1130000	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs1436306	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1436309	0.85[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1436310	0.85[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1539183	0.81[AMR][1000 genomes]
rs1541987	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1800702	0.89[CEU][hapmap];0.94[YRI][hapmap]
rs2006736	0.92[CEU][hapmap];0.94[YRI][hapmap]
rs2013063	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs2032443	0.86[AMR][1000 genomes]
rs2032445	0.86[AMR][1000 genomes]
rs2032449	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2032450	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs2051544	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs2157050	0.96[CEU][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2164485	0.82[ASN][1000 genomes]
rs2164487	0.82[ASN][1000 genomes]
rs2794719	0.84[CEU][hapmap];0.93[YRI][hapmap]
rs2794720	0.88[CEU][hapmap];0.94[YRI][hapmap]
rs3752419	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3752420	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4478388	0.82[ASN][1000 genomes]
rs4529296	0.89[CEU][hapmap];0.94[YRI][hapmap]
rs6928717	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6928951	0.82[AMR][1000 genomes]
rs6929805	0.82[ASN][1000 genomes]
rs6938083	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6942196	0.88[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7738854	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7753253	0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7766342	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7772312	0.89[CEU][hapmap];0.86[AMR][1000 genomes]
rs9295679	0.81[ASN][1000 genomes]
rs9295680	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9295681	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs9295684	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295685	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9295687	0.88[CEU][hapmap];0.93[YRI][hapmap]
rs9295688	0.89[CEU][hapmap]
rs9348704	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9348706	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9358902	0.82[AMR][1000 genomes]
rs9358903	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9358904	0.84[AMR][1000 genomes]
rs9358905	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9366634	0.88[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9379814	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9379815	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9379818	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9379819	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9379820	0.89[CEU][hapmap];0.86[AMR][1000 genomes]
rs9379821	0.88[AMR][1000 genomes]
rs9379825	0.89[CEU][hapmap]
rs9393677	0.82[ASN][1000 genomes]
rs9393678	0.82[ASN][1000 genomes]
rs9393681	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9393683	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393684	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9461227	0.86[ASN][1000 genomes]
rs9461229	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9467641	0.82[ASN][1000 genomes]
rs9467645	0.82[ASN][1000 genomes]
rs9467647	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs9467648	0.82[ASN][1000 genomes]
rs9467650	0.82[ASN][1000 genomes]
rs9467651	0.82[ASN][1000 genomes]
rs9467652	0.85[CHB][hapmap]
rs9467656	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9467658	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9467662	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467663	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467672	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases
8	nsv1015627	chr6:25973495-26100483	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
9	nsv538164	chr6:25973495-26100483	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
10	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
11	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
12	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
13	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
14	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
15	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
16	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9461230	U91328.19	cis	Muscle Skeletal	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26001600-26020600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:26008800-26020600	Weak transcription	Spleen	Spleen
3	chr6:26016200-26019800	Active TSS	Fetal Kidney	kidney
4	chr6:26017400-26020600	ZNF genes & repeats	GM12878-XiMat	blood
5	chr6:26017800-26019800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:26017800-26019800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:26017800-26020600	Weak transcription	Pancreas	Pancrea
8	chr6:26018000-26019800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:26018000-26020200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:26018000-26020600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:26018000-26020600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:26018000-26020600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:26018000-26020600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:26018000-26020600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:26018200-26019400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:26018200-26019400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr6:26018200-26019800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:26018200-26019800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:26018200-26020200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:26018200-26020200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:26018200-26020200	Weak transcription	Fetal Intestine Large	intestine
22	chr6:26018200-26020400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:26018200-26020400	Weak transcription	Thymus	Thymus
24	chr6:26018200-26020600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:26018200-26020600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:26018200-26020600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:26018200-26020600	Weak transcription	Colonic Mucosa	Colon
28	chr6:26018200-26020600	Weak transcription	Esophagus	oesophagus
29	chr6:26018200-26020600	Weak transcription	Gastric	stomach
30	chr6:26018200-26020600	Weak transcription	Ovary	ovary
31	chr6:26018200-26020600	Weak transcription	HSMMtube	muscle
32	chr6:26018400-26019400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr6:26018400-26019800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:26018400-26019800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:26018400-26019800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr6:26018400-26019800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:26018400-26019800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:26018400-26019800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:26018400-26019800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:26018400-26019800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:26018400-26019800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:26018400-26019800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:26018400-26019800	Weak transcription	Adipose Nuclei	Adipose
44	chr6:26018400-26019800	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:26018400-26019800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:26018400-26019800	Weak transcription	Fetal Muscle Leg	muscle
47	chr6:26018400-26019800	Weak transcription	Fetal Stomach	stomach
48	chr6:26018400-26019800	Weak transcription	Fetal Thymus	thymus
49	chr6:26018400-26019800	Weak transcription	Right Atrium	heart
50	chr6:26018400-26019800	Weak transcription	Stomach Smooth Muscle	stomach

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