Variant report

Variant	rs2358774
Chromosome Location	chr1:197664395-197664396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197650384..197656370-chr1:197660434..197666309,6	K562	blood:
2	chr1:197662721..197665578-chr1:197743679..197745656,2	MCF-7	breast:
3	chr1:197653272..197654957-chr1:197663523..197666309,2	K562	blood:

Variant related genes	Relation type
ENSG00000207139	Chromatin interaction
ENSG00000213047	Chromatin interaction

Extended variants
information (count: 194 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:188)

rs_ID	r²[population]
rs10442656	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10442660	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10494758	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10737692	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10754224	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10754225	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10801614	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10922251	0.90[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10922253	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10922255	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10922256	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10922257	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10922258	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10922261	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10922262	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10922288	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs10922292	0.93[ASN][1000 genomes]
rs10922293	0.83[ASN][1000 genomes]
rs12022672	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12025476	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12028758	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12041661	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12116508	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12116519	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12117095	0.93[ASN][1000 genomes]
rs12125739	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12125742	0.83[ASN][1000 genomes]
rs12127369	0.93[ASN][1000 genomes]
rs12127378	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12129043	0.83[ASN][1000 genomes]
rs12131160	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12133885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12563879	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12565840	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12731480	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12740849	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs12740869	0.82[ASN][1000 genomes]
rs12744898	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12747786	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1342694	0.90[CEU][hapmap];0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs1342696	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1362939	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1421397	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1499592	0.83[ASN][1000 genomes]
rs1499593	0.90[CEU][hapmap];0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs1539413	0.95[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1573098	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1573099	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1578718	0.93[ASN][1000 genomes]
rs1578719	0.83[ASN][1000 genomes]
rs1578720	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1592220	0.83[ASN][1000 genomes]
rs1592221	0.83[ASN][1000 genomes]
rs1621898	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1622740	0.95[CEU][hapmap];0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs1622904	0.83[ASN][1000 genomes]
rs1623752	0.83[ASN][1000 genomes]
rs1747811	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1747812	0.83[ASN][1000 genomes]
rs1747814	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1747815	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1747817	0.85[ASN][1000 genomes]
rs1747818	0.94[ASN][1000 genomes]
rs1747820	0.83[ASN][1000 genomes]
rs1747821	0.83[ASN][1000 genomes]
rs1747822	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1747823	0.90[CEU][hapmap];0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs1747824	0.83[ASN][1000 genomes]
rs1747825	0.90[CEU][hapmap];0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs1747826	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1747827	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1747828	0.83[ASN][1000 genomes]
rs17565558	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17622452	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1775441	0.85[ASN][1000 genomes]
rs1775442	0.85[ASN][1000 genomes]
rs1775443	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1775444	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1775445	0.83[ASN][1000 genomes]
rs1775446	0.92[ASN][1000 genomes]
rs1775447	0.81[ASN][1000 genomes]
rs1775450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775451	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1775453	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775454	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1775456	0.95[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1775457	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1775458	0.93[ASN][1000 genomes]
rs1775459	0.93[ASN][1000 genomes]
rs1775460	0.93[ASN][1000 genomes]
rs1775461	0.83[ASN][1000 genomes]
rs1775462	0.93[ASN][1000 genomes]
rs1775463	0.83[ASN][1000 genomes]
rs1775464	0.90[CEU][hapmap];0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs1775465	0.89[CEU][hapmap];0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs1775466	0.95[CEU][hapmap];0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs1775467	0.95[CEU][hapmap];0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs1775468	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1775469	0.90[CEU][hapmap];0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs1775470	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1833464	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1891497	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1924518	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1969	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2016722	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2111931	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2133535	0.83[ASN][1000 genomes]
rs2133536	0.93[ASN][1000 genomes]
rs2147300	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2160969	0.92[ASN][1000 genomes]
rs2193733	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2193734	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2253257	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2265664	0.83[ASN][1000 genomes]
rs2266033	0.83[ASN][1000 genomes]
rs2266034	0.83[ASN][1000 genomes]
rs2266035	0.83[ASN][1000 genomes]
rs2454640	0.93[ASN][1000 genomes]
rs2454641	0.90[ASN][1000 genomes]
rs2477060	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2477063	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2477065	0.82[EUR][1000 genomes]
rs2477066	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2477069	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2477070	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2477071	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2477074	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2477075	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2477076	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2477553	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488387	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488390	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488394	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2488395	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2488396	0.90[CEU][hapmap];0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs2488400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488402	0.83[ASN][1000 genomes]
rs2488403	0.83[ASN][1000 genomes]
rs2488409	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488410	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2488411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497862	0.90[CEU][hapmap];0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs2497863	0.83[ASN][1000 genomes]
rs2649556	0.90[CEU][hapmap];0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs2649557	0.83[ASN][1000 genomes]
rs2797147	0.83[ASN][1000 genomes]
rs34261593	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34548547	0.93[ASN][1000 genomes]
rs35170775	0.83[ASN][1000 genomes]
rs3814321	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4303099	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4316386	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4915248	0.83[ASN][1000 genomes]
rs4915550	0.85[EUR][1000 genomes]
rs4915551	0.81[ASN][1000 genomes]
rs4915552	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4915554	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4915555	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4915557	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4915558	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4915566	0.81[ASN][1000 genomes]
rs55873039	0.83[ASN][1000 genomes]
rs61829272	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61829341	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61830571	0.83[ASN][1000 genomes]
rs6428410	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6428411	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6428412	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6658157	0.93[ASN][1000 genomes]
rs6672023	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6676073	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6676795	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6677361	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6682689	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688993	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689216	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691173	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6697696	0.90[CEU][hapmap];0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs6698921	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6704186	0.89[CEU][hapmap];0.93[ASN][1000 genomes]
rs7523909	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526770	0.82[ASN][1000 genomes]
rs7526846	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7531581	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7538522	0.83[ASN][1000 genomes]
rs7544969	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8179369	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs972405	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv437263	chr1:197599030-197722240	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv873077	chr1:197615391-197698103	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197653000-197665200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:197653000-197665400	Weak transcription	Osteobl	bone
3	chr1:197657000-197677000	Weak transcription	Ovary	ovary
4	chr1:197658000-197665200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:197658200-197668200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:197658400-197665000	Weak transcription	NHEK	skin
7	chr1:197659400-197665200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:197659400-197665800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:197659400-197674800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:197659600-197665200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:197659600-197665600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:197659600-197665600	Weak transcription	K562	blood
13	chr1:197659600-197667000	Weak transcription	Primary B cells from cord blood	blood
14	chr1:197659800-197674400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:197663800-197664400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:197663800-197664400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr1:197663800-197664400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr1:197663800-197664400	Enhancers	Dnd41	blood
19	chr1:197664200-197664400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:197664200-197664400	Enhancers	Primary T helper cells fromperipheralblood	blood

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