Variant report

Variant	rs6736411
Chromosome Location	chr2:63674060-63674061
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	chr2:63664087..63666512-chr2:63673273..63675449,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143951	Chromatin interaction

Extended variants
information (count: 205 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:202)

rs_ID	r²[population]
rs10168545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10170988	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176522	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10207356	0.83[CEU][hapmap]
rs1023820	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1031221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10469944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs10469945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs1082363	0.88[EUR][1000 genomes]
rs10865337	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10865338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10865339	0.89[EUR][1000 genomes]
rs11125957	0.82[CEU][hapmap]
rs11125967	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs11125977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs11125978	0.90[EUR][1000 genomes]
rs112194	0.86[EUR][1000 genomes]
rs11675647	0.83[CEU][hapmap]
rs11684108	0.83[CEU][hapmap]
rs11691718	0.83[CEU][hapmap]
rs11693047	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11693909	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11883730	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs11894445	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs11898615	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12105140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12618974	0.83[CEU][hapmap]
rs12713477	0.83[CEU][hapmap]
rs12713478	0.83[CEU][hapmap]
rs12713494	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713496	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs12990914	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12994711	0.83[CEU][hapmap]
rs13011799	0.83[CEU][hapmap]
rs1356390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400687	0.82[CEU][hapmap]
rs1400688	0.82[CEU][hapmap]
rs1446564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1446565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1446569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs1517404	0.83[CEU][hapmap]
rs1517405	0.82[CEU][hapmap]
rs1550860	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1607205	0.82[CEU][hapmap]
rs166384	0.88[EUR][1000 genomes]
rs17027899	0.80[YRI][hapmap]
rs17027901	0.90[YRI][hapmap]
rs17027902	0.82[YRI][hapmap]
rs17027903	0.90[YRI][hapmap]
rs17027904	0.91[YRI][hapmap]
rs17027906	0.82[YRI][hapmap]
rs174485	0.87[EUR][1000 genomes]
rs1829261	1.00[CHB][hapmap]
rs185499	0.86[EUR][1000 genomes]
rs1867847	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs1867849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs187801	0.85[EUR][1000 genomes]
rs190519	0.83[EUR][1000 genomes]
rs1922421	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs196124	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs196125	0.87[EUR][1000 genomes]
rs2028883	0.90[EUR][1000 genomes]
rs2028887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2030188	0.83[CEU][hapmap]
rs2084200	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2090479	0.83[CEU][hapmap]
rs2121350	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2121351	0.88[EUR][1000 genomes]
rs2166494	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2166497	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2176415	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176416	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs2176417	0.89[CEU][hapmap]
rs2263636	0.82[CEU][hapmap]
rs2292793	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292794	0.82[CEU][hapmap]
rs2292795	0.82[CEU][hapmap]
rs2305157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2421886	0.83[CEU][hapmap]
rs2421887	0.83[CEU][hapmap]
rs2421952	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs2422007	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs2422011	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2604613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs262470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs262471	0.84[EUR][1000 genomes]
rs262472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs262473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs262474	0.85[EUR][1000 genomes]
rs262475	0.87[EUR][1000 genomes]
rs262476	0.87[EUR][1000 genomes]
rs262477	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs262478	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs262479	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs262480	0.87[EUR][1000 genomes]
rs262481	0.85[EUR][1000 genomes]
rs262482	0.86[EUR][1000 genomes]
rs262483	0.86[EUR][1000 genomes]
rs262484	0.87[EUR][1000 genomes]
rs262485	0.87[EUR][1000 genomes]
rs262487	0.86[EUR][1000 genomes]
rs262488	0.86[EUR][1000 genomes]
rs262489	0.83[EUR][1000 genomes]
rs262490	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs262491	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs262493	0.88[EUR][1000 genomes]
rs262495	0.89[EUR][1000 genomes]
rs262501	0.88[EUR][1000 genomes]
rs262502	0.85[EUR][1000 genomes]
rs262503	0.87[EUR][1000 genomes]
rs262504	0.87[EUR][1000 genomes]
rs262505	0.84[EUR][1000 genomes]
rs262506	0.87[EUR][1000 genomes]
rs262507	0.81[EUR][1000 genomes]
rs2677439	0.82[CEU][hapmap]
rs2699389	0.82[CEU][hapmap]
rs2901580	0.82[CEU][hapmap]
rs2901614	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3980466	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4255949	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4671065	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671067	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671068	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671069	0.87[EUR][1000 genomes]
rs4671470	0.83[CEU][hapmap]
rs4671471	0.83[CEU][hapmap]
rs4671472	0.83[CEU][hapmap]
rs4671473	0.83[CEU][hapmap]
rs4671474	0.81[CEU][hapmap]
rs4671476	0.83[CEU][hapmap]
rs4671488	0.89[CEU][hapmap]
rs4671494	0.89[CEU][hapmap]
rs4671503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671508	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671512	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671514	0.88[EUR][1000 genomes]
rs4671515	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4671516	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671517	0.81[EUR][1000 genomes]
rs4671519	0.87[EUR][1000 genomes]
rs6545986	0.82[CEU][hapmap]
rs6546001	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs6546002	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs6546004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546007	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6546009	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6546011	0.83[EUR][1000 genomes]
rs6546016	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6546017	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6546018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6546019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6706123	0.90[EUR][1000 genomes]
rs6706180	0.82[CEU][hapmap]
rs6708804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs6708847	0.83[CEU][hapmap]
rs6709115	0.83[CEU][hapmap]
rs6713500	0.83[CEU][hapmap]
rs6717031	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6717060	0.89[CEU][hapmap]
rs6724044	0.81[CEU][hapmap]
rs6724160	0.89[EUR][1000 genomes]
rs6725694	0.82[CEU][hapmap]
rs6732791	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6734468	0.83[CEU][hapmap]
rs6734648	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6736029	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6738190	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs6741817	0.83[CEU][hapmap]
rs6744720	0.83[CEU][hapmap]
rs6754730	0.85[EUR][1000 genomes]
rs68183503	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7558796	0.83[CEU][hapmap]
rs7563623	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7570031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs7571017	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7571325	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7571697	0.83[CEU][hapmap]
rs7576316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7577952	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7581630	0.81[EUR][1000 genomes]
rs7584404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7591562	0.82[CEU][hapmap]
rs7596446	0.81[CEU][hapmap]
rs7606045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7607257	0.88[EUR][1000 genomes]
rs7608470	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608513	0.90[EUR][1000 genomes]
rs908621	0.83[CEU][hapmap]
rs908622	0.83[CEU][hapmap]
rs9309355	1.00[CHB][hapmap]
rs932171	0.83[CEU][hapmap]
rs932172	0.83[CEU][hapmap]
rs959195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs964880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs964903	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9789351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs989527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv874235	chr2:63622470-63709708	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6736411	MDH1	cis	Adipose Subcutaneous	GTEx
rs6736411	WDPCP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63631800-63675800	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr2:63631800-63677200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:63631800-63681200	Weak transcription	Aorta	Aorta
4	chr2:63631800-63688000	Weak transcription	Right Ventricle	heart
5	chr2:63654600-63678200	Weak transcription	Psoas Muscle	Psoas
6	chr2:63655000-63679000	Weak transcription	Primary T cells from cord blood	blood
7	chr2:63656200-63675600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:63657400-63675400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:63659200-63679200	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:63659600-63679000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:63662000-63698000	Weak transcription	Ovary	ovary
12	chr2:63662200-63681400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:63662800-63688000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:63666400-63688000	Weak transcription	Primary B cells from cord blood	blood
15	chr2:63666600-63726800	Weak transcription	Gastric	stomach
16	chr2:63667000-63680600	Weak transcription	Adipose Nuclei	Adipose
17	chr2:63668200-63684800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:63673200-63674600	Weak transcription	Fetal Heart	heart
19	chr2:63673600-63697800	Weak transcription	Left Ventricle	heart
20	chr2:63673800-63674200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:63673800-63674400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:63673800-63674400	Enhancers	NHEK	skin

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