Variant report

Variant	rs17818461
Chromosome Location	chr12:11864104-11864105
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	chr12:11802553..11805174-chr12:11862801..11866673,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1009951	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1009953	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[EUR][1000 genomes]
rs1009954	0.81[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs10743967	0.85[EUR][1000 genomes]
rs10845407	0.91[EUR][1000 genomes]
rs10845408	0.82[EUR][1000 genomes]
rs11054421	0.85[CEU][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11054423	0.81[CEU][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11054424	0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11054429	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11054433	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs12228191	0.90[EUR][1000 genomes]
rs12369491	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs17818498	0.83[EUR][1000 genomes]
rs17818624	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2051525	0.85[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes]
rs2187641	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2187642	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2416882	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs2416883	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2724588	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2724599	0.82[EUR][1000 genomes]
rs2724600	0.82[EUR][1000 genomes]
rs2724616	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs2724618	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2724635	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs2724645	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[EUR][1000 genomes]
rs2724648	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs2856321	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs2856322	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2856324	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2856338	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2856344	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[EUR][1000 genomes]
rs2860431	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2900208	0.82[EUR][1000 genomes]
rs2954980	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs4763719	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4763720	0.90[EUR][1000 genomes]
rs4763721	0.90[EUR][1000 genomes]
rs7488701	0.90[EUR][1000 genomes]
rs762717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs972798	0.88[CEU][hapmap];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11827400-11879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:11838800-11872200	Weak transcription	Primary T cells from cord blood	blood
3	chr12:11841800-11867400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:11844200-11864600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:11848000-11872200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:11848800-11879600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:11849400-11865000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:11853000-11872000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:11853200-11870400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:11854800-11872600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:11855200-11871800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:11855400-11868200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr12:11857000-11876800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:11857600-11864200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr12:11857800-11865200	Enhancers	Colon Smooth Muscle	Colon
16	chr12:11858600-11870400	Weak transcription	NHLF	lung
17	chr12:11858800-11864600	Weak transcription	HUVEC	blood vessel
18	chr12:11859200-11872000	Weak transcription	HSMMtube	muscle
19	chr12:11859800-11864200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:11860000-11867600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:11860000-11869800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:11860200-11864200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:11860400-11871600	Weak transcription	Placenta	Placenta
24	chr12:11860600-11864200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:11860600-11865000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr12:11860600-11868400	Weak transcription	Fetal Intestine Large	intestine
27	chr12:11860600-11869400	Weak transcription	NH-A	brain
28	chr12:11860800-11864200	Weak transcription	Brain Anterior Caudate	brain
29	chr12:11860800-11864200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:11860800-11864600	Enhancers	Stomach Smooth Muscle	stomach
31	chr12:11860800-11865400	Enhancers	Rectal Smooth Muscle	rectum
32	chr12:11860800-11869400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:11860800-11869400	Weak transcription	Esophagus	oesophagus
34	chr12:11860800-11869400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:11860800-11869600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:11860800-11869800	Weak transcription	Colonic Mucosa	Colon
37	chr12:11860800-11869800	Weak transcription	Fetal Kidney	kidney
38	chr12:11860800-11869800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr12:11860800-11870600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:11860800-11870600	Weak transcription	NHEK	skin
41	chr12:11860800-11871000	Weak transcription	Fetal Brain Male	brain
42	chr12:11860800-11871200	Weak transcription	Lung	lung
43	chr12:11861000-11869800	Weak transcription	HMEC	breast
44	chr12:11861200-11866200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr12:11861200-11866800	Weak transcription	Small Intestine	intestine
46	chr12:11861200-11872400	Strong transcription	Dnd41	blood
47	chr12:11861400-11866800	Weak transcription	Right Atrium	heart
48	chr12:11861400-11869400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr12:11861400-11869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:11861600-11864200	Weak transcription	Fetal Lung	lung

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