Variant report

Variant	rs62415560
Chromosome Location	chr6:76314842-76314843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:75973426..75975778-chr6:76313491..76316125,2	K562	blood:
2	chr6:76314474..76317070-chr6:76320904..76323712,3	MCF-7	breast:
3	chr6:76298381..76301021-chr6:76312234..76315010,2	K562	blood:
4	chr6:76313605..76316318-chr6:76324603..76327531,2	MCF-7	breast:
5	chr6:76314618..76316766-chr6:76326972..76330457,3	K562	blood:
6	chr6:76312246..76314943-chr6:76370644..76373354,2	MCF-7	breast:
7	chr6:76306113..76308673-chr6:76313720..76315996,2	K562	blood:
8	chr6:74160313..74162584-chr6:76312067..76314970,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000112701	Chromatin interaction
ENSG00000217488	Chromatin interaction
ENSG00000164430	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10485375	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751588	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11752694	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11753082	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754482	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11754561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754663	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11755872	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756209	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11758976	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11759036	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1414595	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17414086	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17414687	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17414729	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17414757	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17496664	0.93[ASN][1000 genomes]
rs17497655	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17499394	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17499531	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17792195	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17792285	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17792478	0.87[EUR][1000 genomes]
rs1989367	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133193	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2312929	0.89[ASN][1000 genomes]
rs2313589	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765140	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs45497991	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55749651	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55839204	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55971756	0.93[ASN][1000 genomes]
rs55973299	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56105244	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56173875	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56228311	0.89[ASN][1000 genomes]
rs56343691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414230	0.93[ASN][1000 genomes]
rs62414242	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414244	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414763	0.80[EUR][1000 genomes]
rs62415572	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62415578	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62415581	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62415582	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62415593	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62415595	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62415599	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62415601	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453833	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453835	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66846373	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66926998	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67573572	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6901064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912963	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6913513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918285	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930338	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936085	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs715090	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72884964	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72886846	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72886879	0.83[EUR][1000 genomes]
rs72886897	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72888734	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72888748	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs766244	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7738852	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741113	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7744029	0.86[EUR][1000 genomes]
rs7744412	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745024	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7753896	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762917	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7775832	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9250	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs956653	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv1022428	chr6:76023118-76575620	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv538312	chr6:76023118-76575620	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
5	nsv1032245	chr6:76045537-76545703	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv538313	chr6:76045537-76545703	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
8	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv1023331	chr6:76238459-76482117	Strong transcription ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv538315	chr6:76238459-76482117	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1017542	chr6:76238459-76537447	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
12	nsv1031745	chr6:76257913-76493355	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
13	nsv538316	chr6:76257913-76493355	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
14	nsv533100	chr6:76257914-76493354	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
15	nsv1023749	chr6:76287578-76482117	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
16	nsv538317	chr6:76287578-76482117	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
17	nsv1021090	chr6:76306100-76759397	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv538318	chr6:76306100-76759397	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62415560	SENP6	Cis_1M	lymphoblastoid	RTeQTL
rs62415560	SENP6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76310800-76317600	Active TSS	GM12878-XiMat	blood
2	chr6:76313400-76315600	Enhancers	Primary B cells from peripheral blood	blood
3	chr6:76313600-76315000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:76313600-76320200	Weak transcription	Stomach Mucosa	stomach
5	chr6:76313800-76316000	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr6:76313800-76316600	Weak transcription	Psoas Muscle	Psoas
7	chr6:76313800-76317200	Enhancers	Small Intestine	intestine
8	chr6:76313800-76317400	Weak transcription	Brain Substantia Nigra	brain
9	chr6:76313800-76318800	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr6:76313800-76320200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:76313800-76320200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:76313800-76322200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr6:76313800-76322200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr6:76313800-76325400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:76313800-76331600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:76314000-76315000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:76314000-76315000	Enhancers	Fetal Brain Male	brain
18	chr6:76314000-76315000	Weak transcription	HepG2	liver
19	chr6:76314000-76315600	Enhancers	A549	lung
20	chr6:76314000-76315800	Enhancers	Fetal Heart	heart
21	chr6:76314000-76316200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:76314000-76316200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:76314000-76316600	Weak transcription	Brain Angular Gyrus	brain
24	chr6:76314000-76317400	Weak transcription	Brain Anterior Caudate	brain
25	chr6:76314000-76320200	Weak transcription	Aorta	Aorta
26	chr6:76314000-76321800	Weak transcription	Fetal Intestine Large	intestine
27	chr6:76314000-76323400	Enhancers	Primary T cells from cord blood	blood
28	chr6:76314000-76324600	Weak transcription	Fetal Stomach	stomach
29	chr6:76314000-76325600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:76314000-76325800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr6:76314000-76326000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr6:76314000-76343200	Weak transcription	Fetal Kidney	kidney
33	chr6:76314200-76315000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:76314200-76315000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:76314200-76315000	Enhancers	Ovary	ovary
36	chr6:76314200-76315000	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr6:76314200-76315200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr6:76314200-76315200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:76314200-76315400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
40	chr6:76314200-76315400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:76314200-76315400	Enhancers	Right Ventricle	heart
42	chr6:76314200-76316000	Enhancers	Colon Smooth Muscle	Colon
43	chr6:76314200-76316000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:76314200-76316200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:76314200-76316600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:76314200-76316800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:76314200-76317000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr6:76314200-76317000	Weak transcription	Fetal Brain Female	brain
49	chr6:76314200-76317800	Weak transcription	HUVEC	blood vessel
50	chr6:76314200-76318000	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links