Variant report

Variant	rs2814879
Chromosome Location	chr6:146201743-146201744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:146198677..146204458-chr6:146205817..146210739,7	K562	blood:
2	chr6:146195474..146197660-chr6:146199765..146202378,2	MCF-7	breast:
3	chr6:146197174..146199602-chr6:146199616..146202268,2	K562	blood:
4	chr6:146134557..146137381-chr6:146201371..146203533,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235652	Chromatin interaction
ENSG00000118496	Chromatin interaction

Extended variants
information (count: 199 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:197)

rs_ID	r²[population]
rs1004752	0.80[EUR][1000 genomes]
rs1011596	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1011597	0.85[EUR][1000 genomes]
rs10214925	0.83[EUR][1000 genomes]
rs10223508	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10447449	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1055212	0.85[EUR][1000 genomes]
rs1062067	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1062068	0.88[EUR][1000 genomes]
rs10872580	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11155442	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1133832	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11760	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11965018	0.82[EUR][1000 genomes]
rs12190966	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12199362	0.90[EUR][1000 genomes]
rs13214277	0.87[EUR][1000 genomes]
rs1337841	0.82[EUR][1000 genomes]
rs13437042	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1415746	0.89[EUR][1000 genomes]
rs1415747	0.89[EUR][1000 genomes]
rs1569540	0.83[EUR][1000 genomes]
rs1577916	0.86[EUR][1000 genomes]
rs1832362	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1883365	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1890171	0.88[EUR][1000 genomes]
rs1986729	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2050027	0.86[EUR][1000 genomes]
rs2064185	0.85[EUR][1000 genomes]
rs2092263	0.80[EUR][1000 genomes]
rs2142981	0.89[EUR][1000 genomes]
rs2142983	0.83[EUR][1000 genomes]
rs2243665	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2246334	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2247206	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247211	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247317	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2247429	0.86[EUR][1000 genomes]
rs2247666	0.87[EUR][1000 genomes]
rs2249147	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249386	0.93[EUR][1000 genomes]
rs2250387	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2253194	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253307	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253648	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253654	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2253764	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253768	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253880	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253886	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253887	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254257	0.88[EUR][1000 genomes]
rs2254283	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254288	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2256998	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2265467	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2265468	0.87[EUR][1000 genomes]
rs2265469	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2265471	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2265472	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2265474	0.93[EUR][1000 genomes]
rs2265477	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2265915	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2265916	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2265917	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2265918	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2265919	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328707	0.85[EUR][1000 genomes]
rs2328709	0.90[EUR][1000 genomes]
rs2485632	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2492855	0.82[ASN][1000 genomes]
rs2748500	0.80[ASN][1000 genomes]
rs2748502	0.82[ASN][1000 genomes]
rs2777477	0.82[ASN][1000 genomes]
rs2814880	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811102	0.90[EUR][1000 genomes]
rs3923579	0.85[EUR][1000 genomes]
rs3924498	0.84[EUR][1000 genomes]
rs3924499	0.84[EUR][1000 genomes]
rs3924502	0.85[EUR][1000 genomes]
rs4075694	0.82[EUR][1000 genomes]
rs4075695	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4075696	0.92[ASN][1000 genomes]
rs4243478	0.86[ASN][1000 genomes]
rs4280983	0.82[EUR][1000 genomes]
rs4314514	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4316025	0.97[ASN][1000 genomes]
rs4360151	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4391282	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4435956	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4455694	0.82[EUR][1000 genomes]
rs4566902	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4895683	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4895684	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4896837	0.82[EUR][1000 genomes]
rs4896838	0.82[EUR][1000 genomes]
rs4896839	0.82[EUR][1000 genomes]
rs4896841	0.85[EUR][1000 genomes]
rs4896842	0.86[EUR][1000 genomes]
rs4896843	0.85[EUR][1000 genomes]
rs4896844	0.89[EUR][1000 genomes]
rs4896852	0.82[EUR][1000 genomes]
rs56181683	0.84[ASN][1000 genomes]
rs62435810	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6570713	0.89[EUR][1000 genomes]
rs6570715	0.83[EUR][1000 genomes]
rs6570716	0.81[EUR][1000 genomes]
rs6570717	0.87[EUR][1000 genomes]
rs6570719	0.85[EUR][1000 genomes]
rs6570723	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570724	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6901888	0.83[EUR][1000 genomes]
rs6902913	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6906258	0.89[EUR][1000 genomes]
rs6906402	0.89[EUR][1000 genomes]
rs6910790	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6915718	0.89[EUR][1000 genomes]
rs6917135	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6917482	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6921073	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6922507	0.82[EUR][1000 genomes]
rs6923545	0.83[EUR][1000 genomes]
rs6923678	0.85[EUR][1000 genomes]
rs6926076	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6926657	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6928007	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6931553	0.89[EUR][1000 genomes]
rs6933161	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6937661	0.89[EUR][1000 genomes]
rs697054	0.81[EUR][1000 genomes]
rs697055	0.81[EUR][1000 genomes]
rs697056	0.81[EUR][1000 genomes]
rs702317	0.82[EUR][1000 genomes]
rs702318	0.82[EUR][1000 genomes]
rs702319	0.82[EUR][1000 genomes]
rs702320	0.81[EUR][1000 genomes]
rs702324	0.82[EUR][1000 genomes]
rs735535	0.80[EUR][1000 genomes]
rs735536	0.80[EUR][1000 genomes]
rs7739735	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7740785	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7742333	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7744014	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7745696	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7747576	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7752286	0.89[EUR][1000 genomes]
rs7753092	0.83[EUR][1000 genomes]
rs7753696	0.80[EUR][1000 genomes]
rs7753770	0.85[EUR][1000 genomes]
rs7753833	0.85[EUR][1000 genomes]
rs7762562	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9373473	0.84[ASN][1000 genomes]
rs9373475	0.90[EUR][1000 genomes]
rs9373476	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9376961	0.82[EUR][1000 genomes]
rs9376968	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9376970	0.83[EUR][1000 genomes]
rs9376971	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9386128	0.82[EUR][1000 genomes]
rs9386131	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9386132	0.90[EUR][1000 genomes]
rs9386133	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9386134	0.91[EUR][1000 genomes]
rs9386141	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9390349	0.82[EUR][1000 genomes]
rs9390354	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9390355	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9390356	0.90[EUR][1000 genomes]
rs9390357	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9390358	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9390365	0.84[EUR][1000 genomes]
rs9399564	0.85[EUR][1000 genomes]
rs9399565	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9399567	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9399569	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9399571	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9403741	0.80[EUR][1000 genomes]
rs9403746	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9403747	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403749	0.93[EUR][1000 genomes]
rs9403750	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403755	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403756	0.82[EUR][1000 genomes]
rs9403757	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9485019	0.82[EUR][1000 genomes]
rs9485021	0.82[EUR][1000 genomes]
rs9485024	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9497401	0.85[EUR][1000 genomes]
rs9497406	0.85[EUR][1000 genomes]
rs9497419	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9497424	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9497425	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9497427	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9497431	0.82[EUR][1000 genomes]
rs9497434	0.81[EUR][1000 genomes]
rs9497435	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9791313	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][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	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830835	chr6:146145148-146287473	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2814879	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146172200-146202400	Weak transcription	Adipose Nuclei	Adipose
2	chr6:146177600-146204200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:146185200-146212200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:146186400-146213200	Weak transcription	Brain Anterior Caudate	brain
5	chr6:146188000-146218800	Weak transcription	Right Ventricle	heart
6	chr6:146188800-146209000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:146189200-146202400	Weak transcription	Thymus	Thymus
8	chr6:146189400-146202800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:146189400-146214400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:146189600-146211800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr6:146193400-146207600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:146194000-146211800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:146194200-146202400	Weak transcription	Primary T cells from cord blood	blood
14	chr6:146194800-146212400	Weak transcription	HUVEC	blood vessel
15	chr6:146195000-146209400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:146196200-146210000	Weak transcription	Fetal Brain Male	brain
17	chr6:146196600-146202200	Weak transcription	Left Ventricle	heart
18	chr6:146196600-146202400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:146196600-146202400	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:146196600-146212200	Weak transcription	Aorta	Aorta
21	chr6:146196600-146219600	Weak transcription	HMEC	breast
22	chr6:146196800-146209000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:146197000-146202400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:146197200-146201800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:146197200-146202600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr6:146197200-146209000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:146197400-146203000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:146197600-146202400	Weak transcription	Ovary	ovary
29	chr6:146197800-146219600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:146198000-146202400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:146198000-146204000	Weak transcription	Psoas Muscle	Psoas
32	chr6:146198000-146204000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr6:146198000-146204400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:146198000-146204800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr6:146198000-146209400	Weak transcription	Brain Substantia Nigra	brain
36	chr6:146198000-146209600	Weak transcription	Fetal Brain Female	brain
37	chr6:146198200-146202400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:146198200-146202600	Weak transcription	GM12878-XiMat	blood
39	chr6:146198200-146212400	Weak transcription	Fetal Kidney	kidney
40	chr6:146198200-146218600	Weak transcription	Fetal Heart	heart
41	chr6:146198200-146225600	Weak transcription	HSMMtube	muscle
42	chr6:146198800-146203800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr6:146198800-146207200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:146199200-146203000	Weak transcription	Hela-S3	cervix
45	chr6:146199200-146208800	Weak transcription	Fetal Thymus	thymus
46	chr6:146199400-146202400	Weak transcription	K562	blood
47	chr6:146199600-146209400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:146199800-146202400	Weak transcription	Primary B cells from cord blood	blood
49	chr6:146199800-146202400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:146199800-146203000	Weak transcription	Rectal Smooth Muscle	rectum

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