Variant report

Variant	rs9390354
Chromosome Location	chr6:146108396-146108397
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:146107452..146110586-chr6:146133888..146136897,3	K562	blood:
2	chr6:146054610..146058060-chr6:146107299..146111680,4	K562	blood:
3	chr6:146101702..146103608-chr6:146107062..146109718,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112425	Chromatin interaction
ENSG00000118496	Chromatin interaction
ENSG00000270638	Chromatin interaction
ENSG00000235652	Chromatin interaction

Extended variants
information (count: 215 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:214)

rs_ID	r²[population]
rs1004752	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1011596	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1011597	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10214925	0.90[EUR][1000 genomes]
rs10447449	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1045820	0.83[EUR][1000 genomes]
rs1055212	0.92[EUR][1000 genomes]
rs1062067	0.84[ASN][1000 genomes]
rs1070517	0.81[EUR][1000 genomes]
rs1070519	0.80[EUR][1000 genomes]
rs10872579	0.83[EUR][1000 genomes]
rs10872580	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11155442	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1133832	0.84[ASN][1000 genomes]
rs11760	0.81[ASN][1000 genomes]
rs11965018	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12190966	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12199362	0.95[EUR][1000 genomes]
rs12211884	0.80[EUR][1000 genomes]
rs1292333	0.83[EUR][1000 genomes]
rs1292334	0.83[EUR][1000 genomes]
rs1292336	0.83[EUR][1000 genomes]
rs1292337	0.83[EUR][1000 genomes]
rs1292338	0.80[EUR][1000 genomes]
rs13214277	0.92[EUR][1000 genomes]
rs1337839	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1337840	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1337841	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13437042	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1415744	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1415746	0.95[EUR][1000 genomes]
rs1415747	0.95[EUR][1000 genomes]
rs1569540	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1577916	0.92[EUR][1000 genomes]
rs1832362	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1883365	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1890171	0.93[EUR][1000 genomes]
rs1935616	0.82[EUR][1000 genomes]
rs1986729	0.89[EUR][1000 genomes]
rs2050027	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2064185	0.91[EUR][1000 genomes]
rs2072911	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2092262	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2092263	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2142981	0.94[EUR][1000 genomes]
rs2142983	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2179323	0.83[EUR][1000 genomes]
rs2243665	0.83[ASN][1000 genomes]
rs2246334	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2247206	0.84[ASN][1000 genomes]
rs2247211	0.84[ASN][1000 genomes]
rs2247317	0.84[ASN][1000 genomes]
rs2249147	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2249386	0.92[EUR][1000 genomes]
rs2250387	0.84[ASN][1000 genomes]
rs2253194	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2253307	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2253648	0.85[ASN][1000 genomes]
rs2253654	0.86[EUR][1000 genomes]
rs2253764	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2253768	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2253880	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2253886	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2253887	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2254283	0.84[ASN][1000 genomes]
rs2254288	0.84[ASN][1000 genomes]
rs2256998	0.84[ASN][1000 genomes]
rs2265467	0.83[ASN][1000 genomes]
rs2265469	0.83[ASN][1000 genomes]
rs2265471	0.84[ASN][1000 genomes]
rs2265472	0.83[ASN][1000 genomes]
rs2265474	0.92[EUR][1000 genomes]
rs2265477	0.84[ASN][1000 genomes]
rs2265915	0.88[EUR][1000 genomes]
rs2265916	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2265917	0.84[ASN][1000 genomes]
rs2265918	0.84[ASN][1000 genomes]
rs2265919	0.84[ASN][1000 genomes]
rs2328704	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2328707	0.91[EUR][1000 genomes]
rs2328709	0.96[EUR][1000 genomes]
rs2485632	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814879	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2814880	0.84[ASN][1000 genomes]
rs3811102	0.95[EUR][1000 genomes]
rs4316025	0.82[ASN][1000 genomes]
rs4435956	0.83[ASN][1000 genomes]
rs4455694	0.88[EUR][1000 genomes]
rs4566902	0.83[ASN][1000 genomes]
rs4634475	0.82[EUR][1000 genomes]
rs4895683	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4895684	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4896832	0.83[EUR][1000 genomes]
rs4896833	0.83[EUR][1000 genomes]
rs4896837	0.88[EUR][1000 genomes]
rs4896838	0.88[EUR][1000 genomes]
rs4896839	0.88[EUR][1000 genomes]
rs4896841	0.92[EUR][1000 genomes]
rs4896842	0.91[EUR][1000 genomes]
rs4896843	0.91[EUR][1000 genomes]
rs4896844	0.95[EUR][1000 genomes]
rs55810423	0.86[EUR][1000 genomes]
rs57700188	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62433835	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62435810	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6570701	0.83[EUR][1000 genomes]
rs6570703	0.83[EUR][1000 genomes]
rs6570705	0.83[EUR][1000 genomes]
rs6570706	0.83[EUR][1000 genomes]
rs6570713	0.95[EUR][1000 genomes]
rs6570715	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6570716	0.86[EUR][1000 genomes]
rs6570717	0.93[EUR][1000 genomes]
rs6570719	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6570723	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570724	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6901888	0.89[EUR][1000 genomes]
rs6902913	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906258	0.95[EUR][1000 genomes]
rs6906402	0.95[EUR][1000 genomes]
rs6915718	0.95[EUR][1000 genomes]
rs6917135	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6917482	0.83[ASN][1000 genomes]
rs6921073	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6923678	0.92[EUR][1000 genomes]
rs6926076	0.83[ASN][1000 genomes]
rs6928007	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6930154	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6931553	0.94[EUR][1000 genomes]
rs6932863	0.81[EUR][1000 genomes]
rs6933161	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6937661	0.95[EUR][1000 genomes]
rs697054	0.87[EUR][1000 genomes]
rs697055	0.87[EUR][1000 genomes]
rs697056	0.87[EUR][1000 genomes]
rs702305	0.83[EUR][1000 genomes]
rs702306	0.80[EUR][1000 genomes]
rs702307	0.81[EUR][1000 genomes]
rs702314	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs702317	0.88[EUR][1000 genomes]
rs702318	0.88[EUR][1000 genomes]
rs702319	0.88[EUR][1000 genomes]
rs702320	0.87[EUR][1000 genomes]
rs702321	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs702323	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs702324	0.88[EUR][1000 genomes]
rs735535	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs735536	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7739735	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740785	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7742333	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7744014	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745696	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7752286	0.95[EUR][1000 genomes]
rs7753770	0.92[EUR][1000 genomes]
rs7753833	0.84[EUR][1000 genomes]
rs7762562	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs857875	0.83[EUR][1000 genomes]
rs857877	0.83[EUR][1000 genomes]
rs857879	0.83[EUR][1000 genomes]
rs857880	0.83[EUR][1000 genomes]
rs857882	0.83[EUR][1000 genomes]
rs857883	0.83[EUR][1000 genomes]
rs9373471	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9373473	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9373475	0.95[EUR][1000 genomes]
rs9373476	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9376954	0.82[EUR][1000 genomes]
rs9376956	0.83[EUR][1000 genomes]
rs9376957	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9376961	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9376968	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9386128	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9386131	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386132	0.95[EUR][1000 genomes]
rs9386133	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9386134	0.94[EUR][1000 genomes]
rs9390343	0.81[EUR][1000 genomes]
rs9390344	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9390348	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9390349	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390355	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9390356	0.95[EUR][1000 genomes]
rs9390357	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9390358	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399559	0.83[EUR][1000 genomes]
rs9399564	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9399565	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399567	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9399569	0.82[ASN][1000 genomes]
rs9403737	0.83[EUR][1000 genomes]
rs9403739	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9403741	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9403742	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9403746	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9403747	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9403749	0.92[EUR][1000 genomes]
rs9403750	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9403755	0.83[ASN][1000 genomes]
rs9485018	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9485019	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9485021	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9485024	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9497380	0.83[EUR][1000 genomes]
rs9497395	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9497396	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9497398	0.82[EUR][1000 genomes]
rs9497401	0.92[EUR][1000 genomes]
rs9497406	0.91[EUR][1000 genomes]
rs9497419	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9497424	0.83[ASN][1000 genomes]
rs9497425	0.83[ASN][1000 genomes]
rs9497427	0.81[ASN][1000 genomes]
rs991507	0.86[EUR][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
rs9390354	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146100600-146123200	Weak transcription	HUVEC	blood vessel
2	chr6:146101000-146112200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:146101400-146109400	Weak transcription	Gastric	stomach
4	chr6:146101400-146110000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:146101400-146110800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:146101600-146110000	Weak transcription	Fetal Lung	lung
7	chr6:146101800-146114000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:146102400-146110600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:146103000-146109200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:146103000-146119400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:146103800-146109400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:146104400-146111200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:146104600-146118800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:146104600-146127000	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:146104800-146109600	Weak transcription	Brain Angular Gyrus	brain
16	chr6:146104800-146110200	Weak transcription	Spleen	Spleen
17	chr6:146104800-146111400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:146104800-146112400	Weak transcription	Right Atrium	heart
19	chr6:146105000-146123200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:146105200-146134400	Weak transcription	Thymus	Thymus
21	chr6:146105400-146112000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:146105400-146125800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:146105600-146119000	Weak transcription	NH-A	brain
24	chr6:146105800-146125600	Weak transcription	Fetal Kidney	kidney
25	chr6:146106000-146133600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr6:146106200-146108400	Weak transcription	HSMM	muscle
27	chr6:146106200-146110600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:146106200-146111400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:146106200-146113800	Weak transcription	Dnd41	blood
30	chr6:146106400-146110600	Weak transcription	Fetal Heart	heart
31	chr6:146106600-146111800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:146106600-146118400	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:146106600-146122200	Weak transcription	NHLF	lung
34	chr6:146106800-146109600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:146106800-146109800	Weak transcription	Brain Substantia Nigra	brain
36	chr6:146106800-146110400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:146106800-146121200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:146106800-146122800	Weak transcription	HSMMtube	muscle
39	chr6:146107000-146108800	Weak transcription	Brain Germinal Matrix	brain
40	chr6:146107000-146108800	Weak transcription	Psoas Muscle	Psoas
41	chr6:146107000-146109000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:146107000-146109000	Weak transcription	Fetal Brain Female	brain
43	chr6:146107000-146109000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:146107000-146109600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr6:146107000-146109600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr6:146107000-146109800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:146107000-146109800	Weak transcription	Fetal Stomach	stomach
48	chr6:146107000-146109800	Weak transcription	Pancreas	Pancrea
49	chr6:146107000-146110200	Weak transcription	Ovary	ovary
50	chr6:146107000-146110400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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