Variant report

Variant	rs12199457
Chromosome Location	chr6:76312802-76312803
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74229402..74231607-chr6:76310929..76313785,2	K562	blood:
2	chr6:75952178..75953795-chr6:76311805..76314377,2	K562	blood:
3	chr6:76311042..76312955-chr6:76326997..76330794,3	MCF-7	breast:
4	chr6:76311276..76313926-chr6:76328791..76332406,4	MCF-7	breast:
5	chr6:76312467..76314027-chr6:76330257..76332737,2	K562	blood:
6	chr6:76310925..76313590-chr6:76457201..76459634,2	K562	blood:
7	chr17:62658047..62658828-chr6:76312151..76312940,2	Hela-S3	cervix:
8	chr6:76312117..76313931-chr6:76346420..76348406,2	K562	blood:
9	chr6:76311833..76313694-chr6:76456932..76459481,3	MCF-7	breast:
10	chr6:76298381..76301021-chr6:76312234..76315010,2	K562	blood:
11	chr6:74228897..74233348-chr6:76310739..76313863,5	K562	blood:
12	chr6:75993142..75995708-chr6:76310246..76313188,4	K562	blood:
13	chr17:56735238..56737884-chr6:76312067..76314109,2	MCF-7	breast:
14	chr6:76310839..76313480-chr6:76354672..76356986,2	MCF-7	breast:
15	chr6:76312246..76314943-chr6:76370644..76373354,2	MCF-7	breast:
16	chr6:74160313..74162584-chr6:76312067..76314970,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000156508	Chromatin interaction
ENSG00000112701	Chromatin interaction
ENSG00000225793	Chromatin interaction
ENSG00000108854	Chromatin interaction
ENSG00000196586	Chromatin interaction
ENSG00000112697	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000112695	Chromatin interaction
ENSG00000229862	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10806043	0.81[ASN][1000 genomes]
rs10943253	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs10943273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10943274	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12196108	0.80[ASN][1000 genomes]
rs12199441	0.92[ASN][1000 genomes]
rs12213227	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12524436	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12525161	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13191639	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13214795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1336043	0.81[JPT][hapmap]
rs1414597	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2647400	0.86[JPT][hapmap]
rs2647401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2647402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2647403	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2647409	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2647412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2647413	0.88[EUR][1000 genomes]
rs2647415	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2647418	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2647419	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703662	0.81[JPT][hapmap]
rs2748953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2748965	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2756039	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2783351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2784730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2784732	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2784733	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2808182	0.82[CHB][hapmap]
rs2808186	0.82[JPT][hapmap]
rs2808187	0.82[JPT][hapmap]
rs2842535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2842539	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2842563	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2842571	0.87[EUR][1000 genomes]
rs2842572	0.85[EUR][1000 genomes]
rs2951920	0.81[CHB][hapmap]
rs34239015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35402776	0.80[ASN][1000 genomes]
rs4708189	0.85[YRI][hapmap]
rs478934	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs570939	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs575720	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6453832	0.85[AMR][1000 genomes]
rs649935	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6911868	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6936251	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs7356806	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7768713	0.80[ASN][1000 genomes]
rs9294001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9343290	0.82[JPT][hapmap]
rs9352237	0.92[CEU][hapmap]
rs9443180	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9447503	0.80[ASN][1000 genomes]
rs9447510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9447513	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9447514	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9447522	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9447523	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9447524	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	esv3372148	chr6:76310257-76313105	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12199457	SENP6	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76310400-76314000	Active TSS	Brain Germinal Matrix	brain
2	chr6:76310400-76314400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:76310600-76313400	Active TSS	Brain Cingulate Gyrus	brain
4	chr6:76310600-76313800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:76310600-76313800	Active TSS	Psoas Muscle	Psoas
6	chr6:76310600-76314000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:76310600-76314200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:76310600-76314200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr6:76310800-76313200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:76310800-76313200	Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr6:76310800-76313400	Active TSS	Fetal Thymus	thymus
12	chr6:76310800-76313400	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr6:76310800-76313600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:76310800-76313600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:76310800-76313600	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr6:76310800-76313600	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr6:76310800-76313600	Active TSS	Colon Smooth Muscle	Colon
18	chr6:76310800-76313600	Active TSS	Rectal Smooth Muscle	rectum
19	chr6:76310800-76313800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:76310800-76314000	Active TSS	H1 Cell Line	embryonic stem cell
21	chr6:76310800-76314000	Active TSS	Brain Angular Gyrus	brain
22	chr6:76310800-76314000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr6:76310800-76314000	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr6:76310800-76314000	Active TSS	Fetal Brain Female	brain
25	chr6:76310800-76314000	Active TSS	A549	lung
26	chr6:76310800-76314200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:76310800-76314200	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr6:76310800-76314200	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr6:76310800-76314200	Active TSS	HSMM	muscle
30	chr6:76310800-76314400	Active TSS	Stomach Smooth Muscle	stomach
31	chr6:76310800-76317600	Active TSS	GM12878-XiMat	blood
32	chr6:76311000-76313000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr6:76311000-76313200	Active TSS	Brain Anterior Caudate	brain
34	chr6:76311000-76313200	Active TSS	Dnd41	blood
35	chr6:76311000-76313400	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr6:76311000-76313400	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr6:76311000-76313400	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr6:76311000-76313400	Active TSS	Fetal Brain Male	brain
39	chr6:76311000-76313400	Active TSS	Placenta	Placenta
40	chr6:76311000-76313600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:76311000-76313600	Active TSS	Brain Hippocampus Middle	brain
42	chr6:76311000-76313600	Active TSS	Fetal Muscle Leg	muscle
43	chr6:76311000-76313600	Active TSS	NHEK	skin
44	chr6:76311000-76313800	Active TSS	Fetal Kidney	kidney
45	chr6:76311000-76313800	Active TSS	Fetal Muscle Trunk	muscle
46	chr6:76311000-76313800	Active TSS	HSMMtube	muscle
47	chr6:76311000-76314000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr6:76311000-76314000	Active TSS	Aorta	Aorta
49	chr6:76311000-76314000	Active TSS	Fetal Intestine Large	intestine
50	chr6:76311000-76314000	Active TSS	Fetal Stomach	stomach

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