Variant report

Variant	rs12664312
Chromosome Location	chr6:140398659-140398660
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:140390060..140392664-chr6:140397671..140399616,2	MCF-7	breast:

Extended variants
information (count: 129 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10434888	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10872525	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1119397	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12174980	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12175776	0.83[ASN][1000 genomes]
rs12660474	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12660560	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12662046	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12662151	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12662747	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12663480	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12665797	0.81[ASN][1000 genomes]
rs13191189	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13207048	0.84[ASN][1000 genomes]
rs13215736	0.90[ASN][1000 genomes]
rs1324130	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1496110	0.81[ASN][1000 genomes]
rs1496112	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1496113	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1519592	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1587171	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1603348	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1603349	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17069736	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17069768	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069852	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17069854	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2020197	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34358600	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34753441	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34984534	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35332737	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35392782	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35465283	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36074095	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36126113	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4637665	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56044741	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62431097	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62431100	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62431101	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs66460448	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71562538	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72973906	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7758187	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7761894	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9321765	0.81[ASN][1000 genomes]
rs9373256	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373258	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9373259	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9373260	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9373261	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9373262	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9373266	0.81[ASN][1000 genomes]
rs9376485	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9376493	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9376494	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9376495	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9376496	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9376497	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9376498	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9376500	0.85[EUR][1000 genomes]
rs9376501	0.82[EUR][1000 genomes]
rs9376502	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9376503	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9376504	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9376506	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9385895	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385896	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9385897	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9385899	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9385900	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9385901	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9385902	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9385903	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9385906	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9389741	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389743	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389744	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389745	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9389746	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9389748	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9389749	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389750	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389751	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9389753	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9389754	0.84[ASN][1000 genomes]
rs9389755	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9389757	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9389760	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9389763	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9389767	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9389768	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9389772	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9389773	0.82[EUR][1000 genomes]
rs9389774	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9389776	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9389777	0.84[ASN][1000 genomes]
rs9389780	0.81[ASN][1000 genomes]
rs9389781	0.81[ASN][1000 genomes]
rs9399303	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9399304	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9399305	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399306	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399307	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399308	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9399310	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403135	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9403138	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9403139	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9403143	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9403145	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403146	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403147	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403148	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403149	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9403150	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403151	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403153	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403155	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403156	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403157	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403159	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403165	0.82[ASN][1000 genomes]
rs9484347	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1019508	chr6:140317472-140434466	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1022987	chr6:140344229-140463916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140393000-140399200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:140393000-140399200	Weak transcription	Fetal Intestine Small	intestine
3	chr6:140393000-140399200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:140393000-140399400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:140393000-140400000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:140393000-140400400	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:140393000-140400600	Weak transcription	Ovary	ovary
8	chr6:140393600-140398800	Weak transcription	Fetal Heart	heart
9	chr6:140393600-140400400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:140393800-140399000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:140393800-140399000	Weak transcription	NH-A	brain
12	chr6:140393800-140399200	Weak transcription	Fetal Kidney	kidney
13	chr6:140394000-140398800	Weak transcription	HUVEC	blood vessel
14	chr6:140394000-140400000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:140394400-140399200	Weak transcription	Adipose Nuclei	Adipose
16	chr6:140394400-140403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:140394800-140398800	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:140395000-140398800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:140395000-140398800	Weak transcription	Osteobl	bone
20	chr6:140395000-140399000	Weak transcription	Fetal Lung	lung
21	chr6:140395000-140399200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:140395000-140399400	Weak transcription	Fetal Brain Male	brain
23	chr6:140395000-140400000	Weak transcription	Hela-S3	cervix
24	chr6:140395200-140399000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:140395200-140399000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:140395200-140399400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:140395400-140399200	Weak transcription	Fetal Stomach	stomach
28	chr6:140396600-140399600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:140397000-140399200	Enhancers	NHDF-Ad	bronchial
30	chr6:140398400-140399400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:140398400-140399600	Enhancers	NHLF	lung
32	chr6:140398400-140400800	Enhancers	HSMM	muscle
33	chr6:140398400-140401800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:140398600-140400600	Weak transcription	Left Ventricle	heart

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