Variant report

Variant	rs12337510
Chromosome Location	chr9:21826463-21826464
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	chr9:21803276..21805320-chr9:21825031..21828014,2	MCF-7	breast:
2	chr9:21825303..21827537-chr9:22080207..22082765,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099810	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10217131	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10217379	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10429489	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10511700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10757256	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10811616	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10811619	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10811624	0.81[CEU][hapmap]
rs10811631	0.85[JPT][hapmap]
rs10965124	0.84[ASN][1000 genomes]
rs10965131	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10965150	0.81[CEU][hapmap]
rs10965157	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10965158	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12002238	0.81[ASN][1000 genomes]
rs12002663	0.87[ASN][1000 genomes]
rs12004745	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12336678	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12336734	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12340988	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12348845	0.84[ASN][1000 genomes]
rs12378675	0.80[CEU][hapmap]
rs12379110	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12380313	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12380373	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13286524	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13302653	0.91[CEU][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1414258	0.83[ASN][1000 genomes]
rs1414259	0.83[ASN][1000 genomes]
rs1440992	0.85[ASN][1000 genomes]
rs1544195	0.81[CEU][hapmap]
rs2039971	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2282245	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35235093	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35526535	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3802393	0.82[MEX][hapmap]
rs3931609	0.91[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4295749	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4326466	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4375086	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs4399022	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4543632	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs55656405	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56005066	0.81[ASN][1000 genomes]
rs56237731	0.81[ASN][1000 genomes]
rs56339876	0.81[ASN][1000 genomes]
rs58495931	0.81[ASN][1000 genomes]
rs59990401	0.84[ASN][1000 genomes]
rs61258965	0.81[ASN][1000 genomes]
rs6475575	0.83[ASN][1000 genomes]
rs6475580	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6475581	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6475582	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6475583	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6475584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6475588	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6475589	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66587337	0.82[ASN][1000 genomes]
rs7029287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033148	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7040432	0.84[ASN][1000 genomes]
rs7040895	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7041509	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7042728	0.91[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7042884	0.83[ASN][1000 genomes]
rs7851125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7859886	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7860126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7866362	0.83[ASN][1000 genomes]
rs7866533	0.83[ASN][1000 genomes]
rs7866860	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7867176	0.83[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7868253	0.82[ASN][1000 genomes]
rs7869680	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7871477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7871631	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7874112	0.91[CEU][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs885518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9298826	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs945263	0.83[EUR][1000 genomes];0.87[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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21804000-21838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:21806600-21841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:21809200-21836800	Weak transcription	Small Intestine	intestine
4	chr9:21814000-21831800	Weak transcription	Fetal Heart	heart
5	chr9:21814400-21831800	Weak transcription	Stomach Mucosa	stomach
6	chr9:21814400-21837400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr9:21814400-21845200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:21816400-21836600	Weak transcription	Psoas Muscle	Psoas
9	chr9:21816600-21833800	Weak transcription	Fetal Brain Male	brain
10	chr9:21816800-21833200	Weak transcription	Brain Angular Gyrus	brain
11	chr9:21817400-21829000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:21817400-21830200	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:21817400-21837800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:21817800-21840600	Weak transcription	Colonic Mucosa	Colon
15	chr9:21818600-21840800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:21818800-21840400	Weak transcription	Right Ventricle	heart
17	chr9:21819000-21828800	Weak transcription	HSMMtube	muscle
18	chr9:21819000-21831400	Weak transcription	NHLF	lung
19	chr9:21819200-21827200	Weak transcription	NHDF-Ad	bronchial
20	chr9:21819200-21828800	Weak transcription	Osteobl	bone
21	chr9:21819400-21827400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:21819400-21827600	Weak transcription	NH-A	brain
23	chr9:21819400-21829000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr9:21819400-21829200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:21819400-21830800	Weak transcription	HUVEC	blood vessel
26	chr9:21819400-21831400	Weak transcription	Placenta	Placenta
27	chr9:21819400-21831800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr9:21819400-21833800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:21819400-21840400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr9:21819400-21841600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:21819600-21830600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr9:21819800-21832400	Weak transcription	Brain Anterior Caudate	brain
33	chr9:21823000-21830600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr9:21823800-21826600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:21823800-21826800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:21823800-21840400	Strong transcription	Fetal Muscle Leg	muscle
37	chr9:21824000-21830000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr9:21824000-21830800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:21824000-21831200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:21824200-21826800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr9:21824200-21840400	Strong transcription	Fetal Lung	lung
42	chr9:21824400-21827800	Strong transcription	Esophagus	oesophagus
43	chr9:21824400-21828400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:21824400-21828800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:21824400-21830200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:21824400-21831000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr9:21824400-21831000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr9:21824400-21831200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:21824400-21831400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr9:21824600-21829200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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