Variant report

Variant	rs6767258
Chromosome Location	chr3:88182893-88182894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88177805..88180449-chr3:88180849..88183793,2	K562	blood:
2	chr3:88181347..88191666-chr3:88192147..88201015,17	MCF-7	breast:
3	chr3:88181103..88183005-chr3:88186407..88189257,2	K562	blood:
4	chr3:88172361..88173888-chr3:88181878..88184552,2	K562	blood:
5	chr3:88181730..88183951-chr3:88190920..88192875,2	K562	blood:
6	chr3:88178407..88180770-chr3:88182763..88185697,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175105	Chromatin interaction
ENSG00000229729	Chromatin interaction
ENSG00000163320	Chromatin interaction
ENSG00000179021	Chromatin interaction

Extended variants
information (count: 213 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:212)

rs_ID	r²[population]
rs1006895	0.86[ASN][1000 genomes]
rs1040319	0.89[ASN][1000 genomes]
rs1051413	0.86[ASN][1000 genomes]
rs1051436	0.86[ASN][1000 genomes]
rs1063597	0.86[ASN][1000 genomes]
rs1063603	0.86[ASN][1000 genomes]
rs10865625	0.86[ASN][1000 genomes]
rs11128021	0.94[EUR][1000 genomes]
rs12493327	0.95[EUR][1000 genomes]
rs12631689	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12632529	0.86[ASN][1000 genomes]
rs12714702	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13060704	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13060730	0.86[ASN][1000 genomes]
rs13063511	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13067183	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13067419	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13076170	0.86[ASN][1000 genomes]
rs13098157	0.86[ASN][1000 genomes]
rs13317261	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1991659	0.86[ASN][1000 genomes]
rs2049817	0.86[ASN][1000 genomes]
rs2116149	0.86[ASN][1000 genomes]
rs28672845	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28694532	0.85[ASN][1000 genomes]
rs3732776	0.86[ASN][1000 genomes]
rs3890707	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241551	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4257571	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4276211	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4276212	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4337654	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368523	0.86[ASN][1000 genomes]
rs4374552	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4378991	0.86[ASN][1000 genomes]
rs4384978	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4402954	0.86[EUR][1000 genomes]
rs4407422	0.89[EUR][1000 genomes]
rs4414876	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416403	0.86[ASN][1000 genomes]
rs4429658	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4432672	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4434168	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4438681	0.86[ASN][1000 genomes]
rs4485742	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4488864	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4501136	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4502603	0.86[ASN][1000 genomes]
rs4507280	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4518156	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4555548	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4568164	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4580585	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4588391	0.86[ASN][1000 genomes]
rs4596173	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611846	0.86[ASN][1000 genomes]
rs4616670	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4638995	0.86[ASN][1000 genomes]
rs4858931	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858935	0.90[EUR][1000 genomes]
rs4858936	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858937	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858938	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858981	0.86[ASN][1000 genomes]
rs4858982	0.86[ASN][1000 genomes]
rs4858983	0.86[ASN][1000 genomes]
rs4858985	0.86[ASN][1000 genomes]
rs4858992	0.86[ASN][1000 genomes]
rs4858994	0.86[ASN][1000 genomes]
rs4858995	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858997	0.81[EUR][1000 genomes]
rs4858998	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858999	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859001	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859002	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859004	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859005	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55744603	0.95[EUR][1000 genomes]
rs55923163	0.94[EUR][1000 genomes]
rs55936434	0.94[EUR][1000 genomes]
rs60377014	0.94[EUR][1000 genomes]
rs6419867	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6551268	0.85[ASN][1000 genomes]
rs6551271	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6551272	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6551273	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6551274	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551275	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551277	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551278	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551279	0.86[ASN][1000 genomes]
rs6551280	0.92[EUR][1000 genomes]
rs6551282	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551283	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551284	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551285	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6551286	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6551288	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6551289	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6551291	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6551292	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6551293	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6551294	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6551296	0.85[ASN][1000 genomes]
rs6551297	0.85[ASN][1000 genomes]
rs6551298	0.83[ASN][1000 genomes]
rs6762453	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6771031	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6777019	0.86[ASN][1000 genomes]
rs6778708	0.81[EUR][1000 genomes]
rs6781333	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782507	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6785359	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785560	0.83[ASN][1000 genomes]
rs6786788	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6787824	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6790426	0.86[ASN][1000 genomes]
rs6790629	0.86[ASN][1000 genomes]
rs6791133	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792208	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6793783	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796355	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6799233	0.86[ASN][1000 genomes]
rs6801046	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6804818	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6805804	0.84[ASN][1000 genomes]
rs6805957	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73132515	0.94[EUR][1000 genomes]
rs7427047	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7427296	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7427335	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7427704	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7428357	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7429120	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430158	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7431074	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7432509	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7432838	0.92[EUR][1000 genomes]
rs7433285	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615585	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7617691	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618080	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7618472	0.86[ASN][1000 genomes]
rs7620830	0.94[EUR][1000 genomes]
rs7626777	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7628689	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630028	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7630240	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7632123	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7633121	0.85[ASN][1000 genomes]
rs7635996	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7639420	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641173	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7643923	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7648096	0.86[ASN][1000 genomes]
rs7650707	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651999	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7652528	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7653652	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310066	0.86[ASN][1000 genomes]
rs9310067	0.86[ASN][1000 genomes]
rs9310068	0.86[ASN][1000 genomes]
rs9310072	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9310074	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9310077	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959048	0.86[ASN][1000 genomes]
rs959049	0.86[ASN][1000 genomes]
rs959050	0.86[ASN][1000 genomes]
rs9809661	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9813894	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814057	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9821517	0.86[ASN][1000 genomes]
rs9829873	0.86[ASN][1000 genomes]
rs9831230	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9832011	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9834468	0.92[EUR][1000 genomes]
rs9834501	0.86[ASN][1000 genomes]
rs9835178	0.86[ASN][1000 genomes]
rs9835771	0.86[ASN][1000 genomes]
rs9836364	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9839322	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9840953	0.89[ASN][1000 genomes]
rs9841834	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9843550	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9845776	0.86[ASN][1000 genomes]
rs9846115	0.89[ASN][1000 genomes]
rs9847019	0.86[ASN][1000 genomes]
rs9847355	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9848258	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9849248	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9849353	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9850892	0.86[ASN][1000 genomes]
rs9851328	0.82[ASN][1000 genomes]
rs9854138	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856990	0.85[ASN][1000 genomes]
rs9861398	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9864220	0.86[ASN][1000 genomes]
rs9865335	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865578	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865703	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865710	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865990	0.86[ASN][1000 genomes]
rs9866349	0.86[ASN][1000 genomes]
rs9866843	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9868310	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9868977	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9872602	0.86[ASN][1000 genomes]
rs9873182	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9876807	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9879044	0.85[ASN][1000 genomes]
rs9881255	0.94[EUR][1000 genomes];0.91[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	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6767258	C3orf38	Cis_1M	lymphoblastoid	RTeQTL
rs6767258	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88128800-88198200	Weak transcription	Esophagus	oesophagus
2	chr3:88134800-88188200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:88135600-88196800	Weak transcription	Hela-S3	cervix
4	chr3:88137400-88188200	Weak transcription	Fetal Kidney	kidney
5	chr3:88141000-88197800	Weak transcription	Thymus	Thymus
6	chr3:88145200-88191000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:88145200-88198200	Weak transcription	Aorta	Aorta
8	chr3:88148000-88196400	Weak transcription	Fetal Intestine Small	intestine
9	chr3:88150000-88184600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:88152000-88197000	Weak transcription	Lung	lung
11	chr3:88154800-88183800	Weak transcription	HUVEC	blood vessel
12	chr3:88155400-88188000	Weak transcription	Psoas Muscle	Psoas
13	chr3:88155400-88188200	Weak transcription	Right Ventricle	heart
14	chr3:88155800-88189200	Weak transcription	Colonic Mucosa	Colon
15	chr3:88156000-88189000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:88159600-88197800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:88161000-88197800	Weak transcription	Fetal Stomach	stomach
18	chr3:88161800-88184000	Weak transcription	NH-A	brain
19	chr3:88162200-88188000	Weak transcription	NHLF	lung
20	chr3:88162800-88187800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:88162800-88191600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:88162800-88197200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:88162800-88198000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:88163600-88197800	Weak transcription	Gastric	stomach
25	chr3:88163800-88188400	Weak transcription	Fetal Brain Female	brain
26	chr3:88164200-88188200	Weak transcription	Left Ventricle	heart
27	chr3:88164400-88184000	Weak transcription	HMEC	breast
28	chr3:88165400-88184200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:88165600-88185800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:88165600-88186800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:88165600-88188000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:88166000-88188400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:88166000-88190800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:88166200-88188200	Weak transcription	Fetal Brain Male	brain
35	chr3:88167600-88188400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:88167600-88197800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:88167800-88185800	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:88168000-88197800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:88170400-88184200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:88171000-88198000	Weak transcription	Small Intestine	intestine
41	chr3:88171400-88198000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:88175000-88192000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:88175800-88197800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:88176400-88191800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:88176800-88184000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:88176800-88189200	Weak transcription	K562	blood
47	chr3:88177000-88188200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:88177400-88197800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr3:88178000-88192000	Strong transcription	Dnd41	blood
50	chr3:88178200-88183000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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