Variant report

Variant	rs6937661
Chromosome Location	chr6:146113299-146113300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:146053655..146057107-chr6:146112200..146116878,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112425	Chromatin interaction
ENSG00000270638	Chromatin interaction

Extended variants
information (count: 171 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:170)

rs_ID	r²[population]
rs1004752	0.88[EUR][1000 genomes]
rs1011596	0.93[EUR][1000 genomes]
rs1011597	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10214925	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10447449	0.99[EUR][1000 genomes]
rs1055212	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1062067	0.81[EUR][1000 genomes]
rs1062068	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1070517	0.83[EUR][1000 genomes]
rs1070519	0.82[EUR][1000 genomes]
rs10872580	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11155438	0.81[EUR][1000 genomes]
rs11155442	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1133832	0.80[EUR][1000 genomes]
rs11760	0.81[EUR][1000 genomes]
rs11965018	0.90[EUR][1000 genomes]
rs12190966	0.98[EUR][1000 genomes]
rs12199362	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13214277	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1337839	0.87[EUR][1000 genomes]
rs1337840	0.81[EUR][1000 genomes]
rs1337841	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13437042	0.93[EUR][1000 genomes]
rs1415744	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1415746	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1415747	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1569540	0.91[EUR][1000 genomes]
rs1577916	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1832362	0.96[EUR][1000 genomes]
rs1883365	0.94[EUR][1000 genomes]
rs1890171	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1986729	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2050027	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2064185	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2072911	0.85[EUR][1000 genomes]
rs2092263	0.88[EUR][1000 genomes]
rs2142981	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2142983	0.91[EUR][1000 genomes]
rs2235482	0.81[EUR][1000 genomes]
rs2243665	0.80[EUR][1000 genomes]
rs2246334	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2249147	0.96[EUR][1000 genomes]
rs2249386	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2250387	0.81[EUR][1000 genomes]
rs2253194	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2253307	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2253648	0.80[EUR][1000 genomes]
rs2253654	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2253764	0.89[EUR][1000 genomes]
rs2253768	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2253880	0.89[EUR][1000 genomes]
rs2253886	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2253887	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2254257	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2254283	0.81[EUR][1000 genomes]
rs2254288	0.80[EUR][1000 genomes]
rs2256998	0.81[EUR][1000 genomes]
rs2265474	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265915	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265916	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2328707	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2328709	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485632	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2814879	0.89[EUR][1000 genomes]
rs3811102	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4455694	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4895683	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4895684	0.95[EUR][1000 genomes]
rs4896837	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4896838	0.90[EUR][1000 genomes]
rs4896839	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4896841	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4896842	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4896843	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4896844	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55810423	0.81[EUR][1000 genomes]
rs57700188	0.82[EUR][1000 genomes]
rs62435810	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6570708	0.81[EUR][1000 genomes]
rs6570713	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570715	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570716	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6570717	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570719	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570723	0.96[EUR][1000 genomes]
rs6570724	0.96[EUR][1000 genomes]
rs6901888	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6902913	0.95[EUR][1000 genomes]
rs6906258	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6906402	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6915718	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6917135	0.96[EUR][1000 genomes]
rs6921073	0.98[EUR][1000 genomes]
rs6923678	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6928007	0.94[EUR][1000 genomes]
rs6930154	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6931553	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6932863	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6933161	0.94[EUR][1000 genomes]
rs6941429	0.81[EUR][1000 genomes]
rs697053	0.81[EUR][1000 genomes]
rs697054	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs697055	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs697056	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs702304	0.82[EUR][1000 genomes]
rs702306	0.82[EUR][1000 genomes]
rs702307	0.83[EUR][1000 genomes]
rs702309	0.81[EUR][1000 genomes]
rs702314	0.86[EUR][1000 genomes]
rs702317	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs702318	0.90[EUR][1000 genomes]
rs702319	0.90[EUR][1000 genomes]
rs702320	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs702321	0.87[EUR][1000 genomes]
rs702323	0.87[EUR][1000 genomes]
rs702324	0.90[EUR][1000 genomes]
rs735535	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs735536	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7739735	0.95[EUR][1000 genomes]
rs7740785	0.86[EUR][1000 genomes]
rs7742333	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7744014	0.95[EUR][1000 genomes]
rs7745696	0.96[EUR][1000 genomes]
rs7752286	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7753770	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7753833	0.87[EUR][1000 genomes]
rs7762562	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7772717	0.81[EUR][1000 genomes]
rs857881	0.81[EUR][1000 genomes]
rs9373471	0.83[EUR][1000 genomes]
rs9373473	0.84[EUR][1000 genomes]
rs9373475	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9373476	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9376957	0.87[EUR][1000 genomes]
rs9376961	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9376968	0.96[EUR][1000 genomes]
rs9386128	0.90[EUR][1000 genomes]
rs9386131	0.95[EUR][1000 genomes]
rs9386132	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9386133	0.99[EUR][1000 genomes]
rs9386134	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390348	0.84[EUR][1000 genomes]
rs9390349	0.90[EUR][1000 genomes]
rs9390354	0.95[EUR][1000 genomes]
rs9390355	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390356	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390357	0.90[EUR][1000 genomes]
rs9390358	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9399561	0.81[EUR][1000 genomes]
rs9399564	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9399565	0.94[EUR][1000 genomes]
rs9399567	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403739	0.87[EUR][1000 genomes]
rs9403741	0.88[EUR][1000 genomes]
rs9403742	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9403746	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9403747	0.95[EUR][1000 genomes]
rs9403749	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403750	0.95[EUR][1000 genomes]
rs9485018	0.87[EUR][1000 genomes]
rs9485019	0.90[EUR][1000 genomes]
rs9485021	0.91[EUR][1000 genomes]
rs9485024	0.99[EUR][1000 genomes]
rs9497395	0.87[EUR][1000 genomes]
rs9497396	0.87[EUR][1000 genomes]
rs9497398	0.84[EUR][1000 genomes]
rs9497401	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9497406	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9497419	0.99[EUR][1000 genomes]
rs991507	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6937661	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146100600-146123200	Weak transcription	HUVEC	blood vessel
2	chr6:146101800-146114000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:146103000-146119400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:146104600-146118800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:146104600-146127000	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:146105000-146123200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:146105200-146134400	Weak transcription	Thymus	Thymus
8	chr6:146105400-146125800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:146105600-146119000	Weak transcription	NH-A	brain
10	chr6:146105800-146125600	Weak transcription	Fetal Kidney	kidney
11	chr6:146106000-146133600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:146106200-146113800	Weak transcription	Dnd41	blood
13	chr6:146106600-146118400	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:146106600-146122200	Weak transcription	NHLF	lung
15	chr6:146106800-146121200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:146106800-146122800	Weak transcription	HSMMtube	muscle
17	chr6:146107000-146122200	Weak transcription	Left Ventricle	heart
18	chr6:146107000-146125600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:146109400-146120200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:146110200-146135000	Weak transcription	Pancreas	Pancrea
21	chr6:146110600-146113400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:146110800-146114400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:146111000-146117200	Weak transcription	Fetal Heart	heart
24	chr6:146111000-146120200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:146111400-146113800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:146111600-146116800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:146111800-146114000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:146112200-146113400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:146112400-146113600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:146112400-146113600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:146112400-146118400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:146112400-146122200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:146112400-146122400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:146112400-146122400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:146112400-146122400	Weak transcription	Adipose Nuclei	Adipose
36	chr6:146112400-146123000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr6:146112400-146125400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr6:146112400-146125400	Weak transcription	Fetal Stomach	stomach
39	chr6:146112400-146125600	Weak transcription	Aorta	Aorta
40	chr6:146112400-146125600	Weak transcription	Brain Substantia Nigra	brain
41	chr6:146112400-146135000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:146112600-146118600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:146112600-146121200	Weak transcription	Osteobl	bone
44	chr6:146112600-146122200	Weak transcription	Primary B cells from cord blood	blood
45	chr6:146112600-146124600	Weak transcription	Liver	Liver
46	chr6:146112600-146125800	Weak transcription	Fetal Brain Female	brain
47	chr6:146112800-146114400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:146112800-146122000	Weak transcription	NHEK	skin
49	chr6:146113000-146113800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:146113000-146114200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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