Variant report

Variant	rs7741825
Chromosome Location	chr6:88327338-88327339
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88326068..88328832-chr6:88329382..88333308,3	K562	blood:
2	chr6:88299494..88301783-chr6:88326028..88328470,2	K562	blood:

Variant related genes	Relation type
ENSG00000146282	Chromatin interaction
ENSG00000135336	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1051131	0.91[CHB][hapmap];0.96[JPT][hapmap]
rs1051148	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10755484	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs13193380	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13194003	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13214153	0.82[CHB][hapmap]
rs2207144	0.81[CHB][hapmap]
rs2207146	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2246113	0.82[JPT][hapmap]
rs2268993	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2268994	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2273129	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2284908	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs2300906	0.91[CHB][hapmap];0.96[JPT][hapmap]
rs2300909	0.91[CHB][hapmap];0.96[JPT][hapmap]
rs2307379	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2325064	0.81[ASN][1000 genomes]
rs2754245	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2754247	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2754248	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2754260	0.83[ASN][1000 genomes]
rs2754262	0.82[JPT][hapmap]
rs2787893	0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2787921	0.80[ASN][1000 genomes]
rs2787927	0.82[JPT][hapmap]
rs2787930	0.83[EUR][1000 genomes]
rs2814712	0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3757368	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3918467	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs3934838	0.91[CHB][hapmap];0.96[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4334949	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4464759	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4498321	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4587138	0.87[CHB][hapmap];0.96[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4587143	0.91[CHB][hapmap];0.96[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4706294	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4707373	0.83[ASN][1000 genomes]
rs4707374	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4707376	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707377	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4707379	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4707382	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4707383	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6454631	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6454632	0.81[ASN][1000 genomes]
rs6454636	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6454638	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6454640	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6454641	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6905947	0.82[CHB][hapmap]
rs6906769	0.83[ASN][1000 genomes]
rs6908386	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6914299	0.82[CHB][hapmap]
rs6916732	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6918909	0.83[ASN][1000 genomes]
rs6928160	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6930600	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6931069	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6933587	0.82[CHB][hapmap]
rs6940150	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7742965	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7746465	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7750207	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7752494	0.83[ASN][1000 genomes]
rs7755167	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7757636	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7757794	0.90[ASN][1000 genomes]
rs7761814	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7762864	0.83[ASN][1000 genomes]
rs7772561	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7773906	0.91[CHB][hapmap];0.96[JPT][hapmap];0.83[ASN][1000 genomes]
rs9294379	0.82[CHB][hapmap]
rs9294381	0.82[CHB][hapmap]
rs9444504	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9444512	0.81[ASN][1000 genomes]
rs9444519	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9444522	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9444524	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9444525	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9444526	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9444530	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450701	0.81[CHB][hapmap]
rs9450704	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs9450712	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs9450723	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9450726	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450732	0.91[CHB][hapmap];0.96[JPT][hapmap];0.83[ASN][1000 genomes]
rs9450733	0.82[ASN][1000 genomes]
rs9450738	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450739	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450744	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450752	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450755	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450762	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs985764	0.91[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7741825	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs7741825	SLC35A1	cis	multi-tissue	Pritchard
rs7741825	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs7741825	C6orf166	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88301000-88330200	Weak transcription	Right Ventricle	heart
3	chr6:88301000-88347200	Weak transcription	Small Intestine	intestine
4	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:88301400-88338400	Weak transcription	NHLF	lung
6	chr6:88301400-88354400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:88301400-88354600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:88302000-88347400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:88302000-88354400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:88302000-88354600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:88305200-88329000	Weak transcription	HSMMtube	muscle
13	chr6:88308800-88369800	Weak transcription	Fetal Brain Male	brain
14	chr6:88311400-88334600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:88312200-88371200	Weak transcription	NHEK	skin
16	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
17	chr6:88313800-88338200	Weak transcription	NHDF-Ad	bronchial
18	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
19	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
21	chr6:88315400-88334600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:88316400-88330600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:88316600-88328200	Weak transcription	HUVEC	blood vessel
24	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
26	chr6:88316800-88337800	Weak transcription	GM12878-XiMat	blood
27	chr6:88319000-88333000	Weak transcription	HepG2	liver
28	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:88321200-88348400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:88321400-88327400	Weak transcription	Spleen	Spleen
31	chr6:88321600-88350000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:88322000-88346200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr6:88322000-88352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:88322200-88334400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:88322400-88329400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:88322600-88344800	Weak transcription	HMEC	breast
37	chr6:88322800-88331200	Weak transcription	HSMM	muscle
38	chr6:88322800-88338400	Weak transcription	Osteobl	bone
39	chr6:88322800-88344000	Weak transcription	Liver	Liver
40	chr6:88322800-88344800	Weak transcription	NH-A	brain
41	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr6:88323000-88332400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr6:88323000-88332800	Weak transcription	Brain Angular Gyrus	brain
44	chr6:88323000-88333000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr6:88323000-88342000	Weak transcription	K562	blood
46	chr6:88323000-88344600	Weak transcription	Brain Hippocampus Middle	brain
47	chr6:88323000-88344800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:88323000-88346200	Weak transcription	Fetal Kidney	kidney
49	chr6:88323000-88366400	Weak transcription	A549	lung
50	chr6:88323600-88329600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links