Variant report

Variant	rs2748956
Chromosome Location	chr6:76465003-76465004
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:76463962..76466709-chr6:76471388..76473486,2	MCF-7	breast:
2	chr6:76463940..76466517-chr6:76472497..76474287,2	K562	blood:
3	chr6:76458766..76460644-chr6:76463670..76465363,2	MCF-7	breast:
4	chr6:76458851..76461812-chr6:76463826..76465926,2	K562	blood:
5	chr6:76458851..76461588-chr6:76463826..76466127,2	K562	blood:

Variant related genes	Relation type
ENSG00000196586	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1280044	0.80[CEU][hapmap]
rs1280047	0.81[CEU][hapmap]
rs1321161	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1321162	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2133190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2133191	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647404	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2647405	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2647406	0.81[AMR][1000 genomes]
rs2647408	0.83[ASN][1000 genomes]
rs2647411	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2647417	0.87[AMR][1000 genomes]
rs2748940	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2748943	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2748944	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2748946	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2748947	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2748948	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2748950	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2748954	0.81[AMR][1000 genomes]
rs2748955	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs276696	0.82[ASN][1000 genomes]
rs2842550	0.84[ASN][1000 genomes]
rs2842551	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842553	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2842554	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842558	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2842559	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2842560	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2842561	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3822957	0.80[CEU][hapmap]
rs6903077	0.90[ASN][1000 genomes]
rs6905047	0.80[CEU][hapmap]
rs6906615	0.80[CEU][hapmap]
rs6907476	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6920348	0.86[ASN][1000 genomes]
rs721264	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs9447539	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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
19	nsv886185	chr6:76320846-76498109	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS 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	21 gene(s)	inside rSNPs	diseases
20	nsv886186	chr6:76328955-76469115	Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
21	nsv1032961	chr6:76343575-76788852	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
22	nsv932201	chr6:76365548-77219650	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
23	nsv886187	chr6:76408950-76469115	Strong transcription Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
24	nsv1028340	chr6:76410921-76960225	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
25	nsv538319	chr6:76410921-76960225	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
26	nsv886188	chr6:76411843-76469115	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2748956	SENP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76459600-76472200	Weak transcription	Small Intestine	intestine
2	chr6:76460000-76475600	Weak transcription	Psoas Muscle	Psoas
3	chr6:76460000-76481400	Weak transcription	Aorta	Aorta
4	chr6:76460200-76469000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:76460400-76465200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:76460400-76469000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:76460600-76469000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:76460600-76476800	Weak transcription	Lung	lung
9	chr6:76460800-76469000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:76461000-76480800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:76461000-76485000	Weak transcription	Fetal Stomach	stomach
12	chr6:76461400-76475000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:76461600-76469000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:76461600-76470200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:76461600-76475800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:76461600-76485000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:76462400-76469000	Weak transcription	Left Ventricle	heart
18	chr6:76462400-76482200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:76462600-76467200	Weak transcription	HepG2	liver
20	chr6:76463000-76469000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:76463000-76470200	Weak transcription	Brain Angular Gyrus	brain
22	chr6:76463400-76470600	Weak transcription	Fetal Intestine Large	intestine
23	chr6:76463400-76485200	Weak transcription	Gastric	stomach
24	chr6:76463600-76467200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:76463600-76469000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:76463600-76469000	Weak transcription	HSMM	muscle
27	chr6:76463600-76470200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:76463600-76470400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:76463600-76476000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:76463800-76465200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:76463800-76465400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:76463800-76469000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:76463800-76469000	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:76463800-76473800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:76463800-76478400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:76464000-76465600	Weak transcription	Brain Anterior Caudate	brain
37	chr6:76464000-76467800	Weak transcription	Hela-S3	cervix
38	chr6:76464000-76469000	Weak transcription	Brain Substantia Nigra	brain
39	chr6:76464000-76469000	Weak transcription	GM12878-XiMat	blood
40	chr6:76464000-76469000	Weak transcription	Osteobl	bone
41	chr6:76464000-76470200	Weak transcription	HSMMtube	muscle
42	chr6:76464200-76465400	Weak transcription	NH-A	brain
43	chr6:76464200-76469000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:76464200-76478800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:76464200-76481600	Weak transcription	HUVEC	blood vessel
46	chr6:76464200-76485000	Weak transcription	Pancreas	Pancrea
47	chr6:76464800-76465200	Enhancers	NHDF-Ad	bronchial
48	chr6:76464800-76465800	Weak transcription	NHLF	lung
49	chr6:76464800-76466000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:76465000-76465800	Weak transcription	Fetal Intestine Small	intestine

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