Variant report

Variant	rs10180713
Chromosome Location	chr2:54804693-54804694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54802959..54805853-chr2:54855484..54858345,2	MCF-7	breast:
2	chr2:54797516..54799490-chr2:54803547..54805303,2	K562	blood:
3	chr2:54763015..54764801-chr2:54803765..54806395,2	K562	blood:
4	chr2:54804194..54805987-chr2:54812413..54815195,2	MCF-7	breast:
5	chr2:54781728..54792106-chr2:54796721..54808716,28	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10165490	1.00[YRI][hapmap]
rs1047499	0.95[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11885703	0.83[EUR][1000 genomes]
rs11892788	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11898012	1.00[YRI][hapmap]
rs12104998	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs12105792	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12467581	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12468469	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12617036	0.85[EUR][1000 genomes]
rs12713260	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13016942	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13399435	1.00[YRI][hapmap]
rs1367295	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs1510611	0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1541854	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17344072	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs17521078	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs1864493	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2048371	0.80[EUR][1000 genomes]
rs2271322	0.82[EUR][1000 genomes]
rs2292356	0.92[EUR][1000 genomes]
rs2292357	0.87[EUR][1000 genomes]
rs2931463	0.82[EUR][1000 genomes]
rs2931464	0.82[EUR][1000 genomes]
rs2941583	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2941586	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2941587	0.95[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2941591	0.83[EUR][1000 genomes]
rs2941595	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2971877	0.95[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2971879	0.95[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2971883	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2971887	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3106204	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs354213	0.81[EUR][1000 genomes]
rs354228	0.81[EUR][1000 genomes]
rs354231	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3796014	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4233952	0.80[EUR][1000 genomes]
rs4444573	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4455199	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4519562	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4592889	0.86[EUR][1000 genomes]
rs4671221	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4671222	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs4671225	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4671226	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4671945	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs4671946	0.85[EUR][1000 genomes]
rs4671947	0.85[EUR][1000 genomes]
rs4671949	0.87[EUR][1000 genomes]
rs4671951	0.82[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4671955	0.82[EUR][1000 genomes]
rs4671956	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4671960	0.85[JPT][hapmap]
rs4671961	0.86[JPT][hapmap]
rs4990319	0.85[EUR][1000 genomes]
rs6545418	0.81[EUR][1000 genomes]
rs6545419	0.82[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs6545427	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6545429	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6545434	0.95[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6704769	0.82[EUR][1000 genomes]
rs6706372	0.95[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6724590	0.81[EUR][1000 genomes]
rs6729826	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6731661	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6732949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6734658	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6735813	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6746016	1.00[YRI][hapmap]
rs6746306	0.81[EUR][1000 genomes]
rs6748816	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6760298	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs6761369	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6761398	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7558950	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7563706	0.81[EUR][1000 genomes]
rs7589236	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7607451	0.95[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs907135	0.91[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54795800-54807000	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr2:54795800-54807600	Enhancers	Duodenum Smooth Muscle	Duodenum
3	chr2:54796000-54807600	Enhancers	Brain Angular Gyrus	brain
4	chr2:54796200-54806200	Enhancers	Right Atrium	heart
5	chr2:54796200-54806400	Enhancers	Brain Anterior Caudate	brain
6	chr2:54796200-54806800	Enhancers	Pancreas	Pancrea
7	chr2:54796400-54808800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr2:54796800-54806800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr2:54796800-54807400	Enhancers	Psoas Muscle	Psoas
10	chr2:54796800-54810200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr2:54796800-54810600	Enhancers	Small Intestine	intestine
12	chr2:54797200-54805000	Enhancers	Spleen	Spleen
13	chr2:54797400-54808400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:54797800-54807000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr2:54798600-54805600	Enhancers	NHDF-Ad	bronchial
16	chr2:54798800-54806400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr2:54798800-54806600	Weak transcription	Fetal Brain Male	brain
18	chr2:54799400-54805000	Enhancers	Left Ventricle	heart
19	chr2:54800000-54807400	Enhancers	Right Ventricle	heart
20	chr2:54800200-54805800	Enhancers	NHLF	lung
21	chr2:54800200-54806400	Enhancers	Stomach Mucosa	stomach
22	chr2:54800400-54805000	Genic enhancers	Fetal Muscle Leg	muscle
23	chr2:54800400-54805600	Genic enhancers	HSMM	muscle
24	chr2:54800600-54805400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:54800800-54807000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:54801000-54804800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:54801600-54806200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr2:54801600-54806600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr2:54801600-54808600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:54801800-54806400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:54801800-54806400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:54801800-54806600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:54801800-54806600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr2:54801800-54806600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:54801800-54807400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:54801800-54811000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:54802000-54805200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:54802000-54805400	Enhancers	Duodenum Mucosa	Duodenum
39	chr2:54802000-54806400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr2:54802000-54807000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr2:54802000-54808400	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr2:54802000-54816400	Enhancers	Liver	Liver
43	chr2:54802200-54805200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:54802200-54806600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:54802200-54822600	Weak transcription	Esophagus	oesophagus
46	chr2:54802400-54805400	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr2:54802400-54808600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:54802600-54805400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:54802600-54805600	Enhancers	Gastric	stomach
50	chr2:54802600-54806400	Enhancers	Colonic Mucosa	Colon

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