Variant report

Variant	rs2254465
Chromosome Location	chr1:180257692-180257693
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180256674..180259200-chr1:180261718..180263635,2	MCF-7	breast:
2	chr1:180245403..180247439-chr1:180257140..180259358,2	MCF-7	breast:
3	chr1:180256515..180258678-chr1:180261672..180263403,2	K562	blood:
4	chr1:180252603..180254797-chr1:180256198..180258303,3	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10494528	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs10494529	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs1069436	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913988	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs10913991	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs10913992	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs10913995	0.81[EUR][1000 genomes]
rs10913996	0.83[EUR][1000 genomes]
rs10914004	0.83[EUR][1000 genomes]
rs11487431	0.83[EUR][1000 genomes]
rs12070624	0.83[EUR][1000 genomes]
rs12071353	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs12076995	0.83[EUR][1000 genomes]
rs12077656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12081494	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs12083900	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs12084039	0.83[EUR][1000 genomes]
rs12087325	0.83[EUR][1000 genomes]
rs12089373	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs2764433	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764460	0.89[EUR][1000 genomes]
rs357044	1.00[CEU][hapmap]
rs357047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4403592	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs55660948	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55962675	0.83[EUR][1000 genomes]
rs56333717	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57424497	0.83[EUR][1000 genomes]
rs57493263	0.83[EUR][1000 genomes]
rs58145394	0.81[EUR][1000 genomes]
rs58369506	0.83[EUR][1000 genomes]
rs59357483	0.83[EUR][1000 genomes]
rs60528279	0.88[EUR][1000 genomes]
rs61024380	0.83[EUR][1000 genomes]
rs6425635	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs66619942	0.83[EUR][1000 genomes]
rs6663823	0.87[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs6667388	0.83[EUR][1000 genomes]
rs6670242	0.83[EUR][1000 genomes]
rs6670868	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670950	0.87[CEU][hapmap]
rs6673113	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6676778	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs66913400	0.83[EUR][1000 genomes]
rs6696075	0.83[EUR][1000 genomes]
rs67071426	0.83[EUR][1000 genomes]
rs67621570	0.83[EUR][1000 genomes]
rs67716213	0.83[EUR][1000 genomes]
rs67830766	0.83[EUR][1000 genomes]
rs72714809	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714814	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714815	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714816	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72714819	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714820	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714824	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714859	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714872	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714883	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714890	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714891	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714892	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714894	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714896	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72716605	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72716619	0.85[EUR][1000 genomes]
rs72716624	0.85[EUR][1000 genomes]
rs72716634	0.87[ASN][1000 genomes]
rs73037411	0.83[EUR][1000 genomes]
rs73048237	0.83[EUR][1000 genomes]
rs7533389	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542223	0.87[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7552701	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9662762	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv466239	chr1:180145978-180268476	Bivalent Enhancer ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv548345	chr1:180145978-180268476	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers 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
8	nsv498075	chr1:180179441-180278544	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180240200-180259000	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:180240800-180258200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:180240800-180259400	Weak transcription	HepG2	liver
4	chr1:180240800-180264000	Weak transcription	Small Intestine	intestine
5	chr1:180240800-180270800	Weak transcription	NHLF	lung
6	chr1:180241000-180259600	Weak transcription	NH-A	brain
7	chr1:180242000-180268400	Weak transcription	NHDF-Ad	bronchial
8	chr1:180243800-180268200	Weak transcription	Pancreas	Pancrea
9	chr1:180244200-180257800	Weak transcription	Brain Germinal Matrix	brain
10	chr1:180244200-180258200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:180244200-180258400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:180244200-180263000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:180244200-180270400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:180244200-180278200	Weak transcription	HSMMtube	muscle
15	chr1:180245000-180259800	Weak transcription	Colonic Mucosa	Colon
16	chr1:180245200-180258200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:180245200-180259200	Weak transcription	Spleen	Spleen
18	chr1:180245200-180261600	Weak transcription	Right Ventricle	heart
19	chr1:180245200-180282400	Weak transcription	Fetal Intestine Large	intestine
20	chr1:180245400-180268200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:180245400-180280400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:180246400-180258000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:180246800-180264200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:180247600-180262000	Weak transcription	Aorta	Aorta
25	chr1:180247800-180258800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:180247800-180259200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:180247800-180259200	Weak transcription	Psoas Muscle	Psoas
28	chr1:180247800-180260000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:180247800-180263800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:180247800-180284200	Weak transcription	Fetal Thymus	thymus
31	chr1:180248000-180258200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:180248000-180263000	Weak transcription	Fetal Intestine Small	intestine
33	chr1:180248000-180263800	Weak transcription	Placenta	Placenta
34	chr1:180248000-180266800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:180248800-180276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:180249000-180260400	Weak transcription	HUVEC	blood vessel
37	chr1:180250400-180279800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:180250600-180258200	Weak transcription	A549	lung
39	chr1:180250600-180259200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:180250600-180261800	Weak transcription	Lung	lung
41	chr1:180250600-180278600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:180250800-180258200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:180250800-180258600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:180251800-180260000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr1:180252000-180260000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:180252200-180257800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:180252600-180258600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:180254200-180257800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:180254400-180280400	Weak transcription	Fetal Stomach	stomach
50	chr1:180254600-180266200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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