Variant report

Variant	rs3969287
Chromosome Location	chr6:76404030-76404031
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:76402029..76404149-chr6:76408590..76410105,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10943264	0.87[AFR][1000 genomes]
rs12175393	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs1280235	0.84[AFR][1000 genomes]
rs2173402	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647400	0.91[CEU][hapmap]
rs276683	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs276685	0.86[CHB][hapmap];0.83[YRI][hapmap]
rs276687	0.86[CHB][hapmap]
rs2872311	0.85[AFR][1000 genomes]
rs34489326	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471638	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs472458	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs504323	0.93[CHB][hapmap]
rs518622	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs518969	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs523465	0.93[CHB][hapmap]
rs567903	0.93[CHB][hapmap]
rs583781	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs584677	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs594804	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs613562	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618239	0.93[CHB][hapmap]
rs619786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs619920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6453837	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs646967	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6921970	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6931578	0.92[CHB][hapmap]
rs6937154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs7385	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775060	0.93[CHB][hapmap]
rs7771393	0.87[AFR][1000 genomes]
rs9343313	0.92[CHB][hapmap]
rs9343314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9343316	0.93[CHB][hapmap]
rs9343317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9343318	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352219	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs9359132	0.93[CHB][hapmap]
rs9360934	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9360935	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	nsv886184	chr6:76320846-76462711	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
20	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
21	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
22	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
23	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
24	nsv522814	chr6:76375321-76405700	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	esv3335869	chr6:76389281-76411862	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
26	esv3332890	chr6:76390281-76414581	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3969287	SENP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76382000-76422800	Weak transcription	Stomach Mucosa	stomach
2	chr6:76390000-76405600	Weak transcription	HMEC	breast
3	chr6:76391000-76406800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:76391400-76410400	Weak transcription	Brain Substantia Nigra	brain
5	chr6:76391400-76417200	Weak transcription	Gastric	stomach
6	chr6:76391400-76421200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:76391400-76426600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:76391600-76419200	Weak transcription	Right Ventricle	heart
9	chr6:76391600-76427200	Weak transcription	Small Intestine	intestine
10	chr6:76392000-76405600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:76392000-76405600	Weak transcription	Hela-S3	cervix
12	chr6:76392000-76406000	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:76392000-76406200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:76392000-76406600	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:76392000-76407000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:76392000-76410000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:76392000-76410400	Weak transcription	Brain Angular Gyrus	brain
18	chr6:76392000-76412200	Weak transcription	HepG2	liver
19	chr6:76392000-76412400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr6:76392000-76421400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:76392000-76423400	Weak transcription	NHEK	skin
22	chr6:76392000-76423800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr6:76392200-76405000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:76392200-76405600	Weak transcription	Primary B cells from cord blood	blood
25	chr6:76392200-76405600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:76392200-76406200	Weak transcription	A549	lung
27	chr6:76392200-76407600	Weak transcription	Fetal Brain Male	brain
28	chr6:76392200-76407800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:76392200-76420400	Weak transcription	Fetal Heart	heart
30	chr6:76392200-76421000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:76392200-76426800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr6:76392400-76405600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:76392400-76405600	Weak transcription	Fetal Kidney	kidney
34	chr6:76392400-76406000	Weak transcription	Brain Anterior Caudate	brain
35	chr6:76392400-76406200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:76393000-76409800	Weak transcription	Psoas Muscle	Psoas
37	chr6:76393200-76405800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:76395200-76420200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:76396800-76414600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:76396800-76414600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr6:76396800-76414800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:76397000-76405000	Strong transcription	Fetal Stomach	stomach
43	chr6:76397000-76411400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:76397000-76413400	Strong transcription	Fetal Thymus	thymus
45	chr6:76397200-76415800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:76397200-76418000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:76397400-76413600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:76397400-76414000	Strong transcription	Dnd41	blood
49	chr6:76397400-76415000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:76397400-76430800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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