Variant report

Variant	rs4715657
Chromosome Location	chr6:57194118-57194119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:57184109..57185924-chr6:57191382..57194380,2	K562	blood:
2	chr6:57188094..57190184-chr6:57192296..57194436,2	MCF-7	breast:
3	chr6:57182975..57187891-chr6:57191602..57197743,6	K562	blood:
4	chr6:57189628..57192491-chr6:57192735..57194263,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1013893	0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1013894	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1019210	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap]
rs1029872	0.86[CHB][hapmap]
rs10733187	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs1119375	0.91[CHB][hapmap];0.89[CHD][hapmap]
rs12664535	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs1618210	0.93[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1741916	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs1755833	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2013464	0.83[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2013480	0.87[CHB][hapmap]
rs2098172	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs2191651	0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap]
rs2215511	0.86[CHB][hapmap]
rs3800015	0.95[CHB][hapmap]
rs4288209	0.86[CHB][hapmap];0.88[GIH][hapmap]
rs4712144	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.82[ASN][1000 genomes]
rs4712154	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[MEX][hapmap]
rs4715653	0.88[ASN][1000 genomes]
rs4715654	0.91[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.80[ASN][1000 genomes]
rs4715655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715656	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs6459191	0.81[ASN][1000 genomes]
rs6459193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs7738530	0.86[CHB][hapmap]
rs7748584	0.81[CHB][hapmap]
rs7754116	0.86[ASN][1000 genomes]
rs7756422	0.86[CHB][hapmap]
rs7771738	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs9357943	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357944	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs9382701	0.88[ASN][1000 genomes]
rs9382736	0.90[CHB][hapmap]
rs9396278	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap]
rs9464439	0.89[ASN][1000 genomes]
rs980327	0.95[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2758056	chr6:57184541-57562604	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	esv2759432	chr6:57184541-57562604	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1034139	chr6:57192993-57253423	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1022055	chr6:57192993-57353692	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4715657	PRIM2	cis	multi-tissue	Pritchard
rs4715657	GUSBL2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57182800-57194200	Weak transcription	Small Intestine	intestine
2	chr6:57183000-57194200	Weak transcription	Pancreas	Pancrea
3	chr6:57183000-57194200	Weak transcription	Spleen	Spleen
4	chr6:57183000-57194400	Weak transcription	Brain Substantia Nigra	brain
5	chr6:57183000-57194600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:57183000-57199400	Weak transcription	HSMMtube	muscle
7	chr6:57183200-57194400	Weak transcription	Psoas Muscle	Psoas
8	chr6:57183200-57199200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:57183800-57194200	Strong transcription	Fetal Thymus	thymus
10	chr6:57184000-57194600	Strong transcription	Primary B cells from cord blood	blood
11	chr6:57184000-57195800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:57184200-57194400	Weak transcription	Fetal Heart	heart
13	chr6:57184200-57201200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:57184600-57194400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:57184600-57196000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:57184600-57196200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:57184600-57199200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:57184800-57194400	Strong transcription	HepG2	liver
19	chr6:57184800-57194800	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr6:57184800-57199600	Strong transcription	HSMM	muscle
21	chr6:57185000-57195000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr6:57185200-57194400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr6:57185200-57195800	Strong transcription	Osteobl	bone
24	chr6:57186000-57194200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:57186400-57194200	Weak transcription	Right Ventricle	heart
26	chr6:57187400-57196600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:57188800-57194800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr6:57189400-57195200	Strong transcription	Hela-S3	cervix
29	chr6:57189800-57194600	Strong transcription	Fetal Intestine Large	intestine
30	chr6:57190000-57194200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:57190000-57194200	Strong transcription	Adipose Nuclei	Adipose
32	chr6:57190000-57195000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:57190000-57195000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr6:57190000-57199800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:57190000-57200000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:57190200-57194200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr6:57190200-57194600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:57190200-57194600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:57190200-57194800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr6:57190200-57194800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr6:57190200-57195000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:57190400-57194200	Strong transcription	Colon Smooth Muscle	Colon
43	chr6:57190600-57194200	Strong transcription	A549	lung
44	chr6:57190600-57195000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:57190800-57194200	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:57190800-57194400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr6:57191200-57194200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr6:57191200-57194400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr6:57191800-57199800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:57192000-57194200	Strong transcription	Primary hematopoietic stem cells	blood

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