Variant report

Variant	rs2748957
Chromosome Location	chr6:76475333-76475334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:76458866..76461215-chr6:76472496..76475519,3	MCF-7	breast:
2	chr6:76457060..76461197-chr6:76473704..76478813,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196586	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10485375	1.00[CHB][hapmap]
rs10498904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11752694	0.83[ASN][1000 genomes]
rs11753082	1.00[CHB][hapmap]
rs11753849	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11754561	1.00[CHB][hapmap]
rs11754663	0.83[ASN][1000 genomes]
rs11755704	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11755872	1.00[CHB][hapmap]
rs11756209	0.83[ASN][1000 genomes]
rs11758543	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11758976	0.83[ASN][1000 genomes]
rs11759036	0.83[ASN][1000 genomes]
rs12606	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12664049	0.80[CEU][hapmap]
rs1280038	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280040	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280050	0.85[CHB][hapmap]
rs1280053	0.85[CHB][hapmap]
rs1280054	0.85[CHB][hapmap]
rs1280058	0.82[CHB][hapmap]
rs17189990	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191306	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17192223	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17192279	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17414086	1.00[CHB][hapmap]
rs17414687	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17414729	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17414757	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17499394	1.00[CHB][hapmap]
rs17499531	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17792195	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17792285	0.83[ASN][1000 genomes]
rs17794529	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17800625	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2104203	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2133193	0.83[ASN][1000 genomes]
rs2295936	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2748960	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748963	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748966	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842543	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842545	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842547	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3798425	0.85[CEU][hapmap]
rs3798434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3798435	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3818310	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56006932	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56173875	0.80[ASN][1000 genomes]
rs57920948	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61237402	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62414763	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62414769	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62414787	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62414789	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62414791	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62414798	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62414800	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62414802	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62414803	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62414804	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62414824	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62415593	0.83[ASN][1000 genomes]
rs62415599	0.83[ASN][1000 genomes]
rs62415601	0.83[ASN][1000 genomes]
rs6453835	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66846373	0.83[ASN][1000 genomes]
rs66926998	0.83[ASN][1000 genomes]
rs67573572	0.83[ASN][1000 genomes]
rs6904567	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6912963	0.83[ASN][1000 genomes]
rs6936085	0.83[ASN][1000 genomes]
rs72886897	0.83[ASN][1000 genomes]
rs72888734	0.83[ASN][1000 genomes]
rs72888748	0.80[ASN][1000 genomes]
rs72890660	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766244	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7741113	0.83[ASN][1000 genomes]
rs7748145	0.82[AMR][1000 genomes]
rs7761004	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7762917	0.80[ASN][1000 genomes]
rs7773977	0.82[AMR][1000 genomes]
rs7775832	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs9250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs956653	1.00[CHB][hapmap]
rs999209	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
21	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
22	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
23	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2748957	SENP6	cis	Whole Blood	GTEx
rs2748957	SENP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76460000-76475600	Weak transcription	Psoas Muscle	Psoas
2	chr6:76460000-76481400	Weak transcription	Aorta	Aorta
3	chr6:76460600-76476800	Weak transcription	Lung	lung
4	chr6:76461000-76480800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:76461000-76485000	Weak transcription	Fetal Stomach	stomach
6	chr6:76461600-76475800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:76461600-76485000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:76462400-76482200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:76463400-76485200	Weak transcription	Gastric	stomach
10	chr6:76463600-76476000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:76463800-76478400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:76464200-76478800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:76464200-76481600	Weak transcription	HUVEC	blood vessel
14	chr6:76464200-76485000	Weak transcription	Pancreas	Pancrea
15	chr6:76469400-76477800	Weak transcription	GM12878-XiMat	blood
16	chr6:76469400-76484800	Weak transcription	Left Ventricle	heart
17	chr6:76469400-76485200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:76470000-76485000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:76470200-76483200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:76470800-76475400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:76470800-76481200	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:76470800-76486400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:76471000-76481800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:76472400-76478600	Weak transcription	Fetal Intestine Large	intestine
25	chr6:76472400-76485000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:76472600-76476400	Weak transcription	Right Ventricle	heart
27	chr6:76472600-76480600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:76472600-76484600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:76472600-76528000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:76474000-76483000	Weak transcription	Brain Anterior Caudate	brain
31	chr6:76474600-76491000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:76474800-76475600	Weak transcription	Fetal Intestine Small	intestine

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