Variant report

Variant	rs6977895
Chromosome Location	chr7:5052357-5052358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:5052294-5052391	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000270822	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10085591	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10215776	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10226147	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10229468	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10238244	0.85[CEU][hapmap]
rs10240940	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10245090	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10272726	0.84[CEU][hapmap];0.85[AMR][1000 genomes]
rs10275581	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10951759	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10951760	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10951761	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1127434	0.81[CEU][hapmap]
rs11971044	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11971647	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12668514	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12670409	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12672515	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13240149	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28449930	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35013001	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35876367	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36039016	0.82[AMR][1000 genomes]
rs4268029	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4363098	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4364532	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4380823	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4403324	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs4419727	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4431493	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4538789	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4585633	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs56274918	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61116960	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61296609	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6463220	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6463228	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6463238	0.84[CEU][hapmap]
rs6942686	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6946374	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6960279	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6960304	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6971154	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7778009	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7778444	0.81[CEU][hapmap]
rs7779828	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7780676	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7781429	0.80[AMR][1000 genomes]
rs7782190	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7786822	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7787140	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7788954	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7793124	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7794361	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7794683	0.84[CEU][hapmap]
rs7800799	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7802223	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9769483	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9886313	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv8033	chr7:4802287-5086597	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1022678	chr7:4810626-5113387	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv538705	chr7:4810626-5113387	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1021170	chr7:4831361-5058033	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv538706	chr7:4831361-5058033	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1033855	chr7:4862677-5069764	Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
12	nsv1019120	chr7:4929653-5138409	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
13	nsv917078	chr7:4962123-5151633	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv525289	chr7:5003373-5083741	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	nsv966749	chr7:5036761-5098568	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5029800-5059400	Weak transcription	NHDF-Ad	bronchial
2	chr7:5036600-5064200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:5037000-5054400	Weak transcription	Small Intestine	intestine
4	chr7:5037000-5058600	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:5037200-5059400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:5037600-5062000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:5037600-5064800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr7:5038000-5061400	Weak transcription	HSMMtube	muscle
9	chr7:5038200-5066000	Weak transcription	Brain Substantia Nigra	brain
10	chr7:5038800-5067600	Weak transcription	Gastric	stomach
11	chr7:5038800-5085000	Weak transcription	Spleen	Spleen
12	chr7:5039000-5058600	Weak transcription	Brain Angular Gyrus	brain
13	chr7:5039000-5076200	Weak transcription	Brain Anterior Caudate	brain
14	chr7:5039000-5078400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:5039200-5060400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr7:5039400-5059200	Weak transcription	Thymus	Thymus
17	chr7:5039400-5085000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:5040000-5054000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:5040200-5059600	Weak transcription	Adipose Nuclei	Adipose
20	chr7:5041800-5066200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:5043000-5058600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr7:5045000-5063400	Weak transcription	Pancreas	Pancrea
23	chr7:5045400-5065200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:5045800-5059000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:5045800-5059400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:5045800-5059800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr7:5047600-5063600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr7:5048200-5059000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr7:5049000-5056800	Weak transcription	Primary B cells from cord blood	blood
30	chr7:5049000-5061400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:5049200-5059000	Weak transcription	Ovary	ovary
32	chr7:5049400-5060600	Weak transcription	A549	lung
33	chr7:5049400-5061400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:5049400-5072200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr7:5049600-5059000	Weak transcription	Dnd41	blood
36	chr7:5049800-5057800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:5049800-5064000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr7:5050000-5052400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr7:5050000-5052400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr7:5050200-5065400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:5050600-5066800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr7:5050600-5071800	Weak transcription	Brain Hippocampus Middle	brain
43	chr7:5051000-5059000	Weak transcription	Primary T cells from cord blood	blood
44	chr7:5051000-5059000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:5051000-5059800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr7:5051000-5059800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:5051000-5062400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr7:5051000-5067000	Weak transcription	Fetal Lung	lung
49	chr7:5051200-5057000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:5051200-5057000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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