Variant report

Variant	rs12257917
Chromosome Location	chr10:43896207-43896208
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	chr10:43895990-43896324	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:43888984-43898060	K562	blood:	n/a	n/a
3	POLR2A	chr10:43895689-43896409	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:43896003-43896590	K562	blood:	n/a	n/a
5	POLR2A	chr10:43894070-43896282	HepG2	liver:	n/a	n/a
6	POLR2A	chr10:43896022-43896411	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr10:43896004-43896332	GM12891	blood:	n/a	n/a
8	POLR2A	chr10:43896038-43896375	K562	blood:	n/a	n/a
9	POLR2A	chr10:43894150-43896238	K562	blood:	n/a	n/a
10	POLR2A	chr10:43894064-43898053	K562	blood:	n/a	n/a
11	POLR2A	chr10:43878581-43905107	K562	blood:	n/a	n/a
12	POLR2A	chr10:43896174-43896359	MCF-7	breast:	n/a	n/a
13	POLR2A	chr10:43895905-43896355	GM12892	blood:	n/a	n/a
14	POLR2A	chr10:43896043-43896371	GM12891	blood:	n/a	n/a
15	POLR2A	chr10:43891015-43896319	K562	blood:	n/a	n/a
16	POLR2A	chr10:43894101-43899596	HepG2	liver:	n/a	n/a
17	POLR2A	chr10:43896117-43896293	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr10:43893441-43899649	A549	lung:	n/a	n/a
19	POLR2A	chr10:43896001-43896365	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43887055..43906178-chr10:43946385..43955803,85	K562	blood:

Variant related genes	Relation type
HNRNPF	TF binding region
ENSG00000252532	Chromatin interaction
ENSG00000243660	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10793431	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10899794	0.88[ASN][1000 genomes]
rs10899797	0.96[ASN][1000 genomes]
rs10899798	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10899799	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11238526	0.95[ASN][1000 genomes]
rs1126709	0.99[ASN][1000 genomes]
rs1416226	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17153606	0.80[EUR][1000 genomes]
rs2066043	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2066044	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2247860	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2247979	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247981	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2248332	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2248335	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2248469	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2248931	0.80[ASN][1000 genomes]
rs2250444	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2252783	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2252785	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2252800	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252804	0.90[AFR][1000 genomes]
rs2255967	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256495	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2260200	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2261636	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2265886	0.85[AFR][1000 genomes]
rs2265887	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2265888	0.81[AFR][1000 genomes]
rs2265952	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2265953	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265954	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2460558	0.88[ASN][1000 genomes]
rs2492404	0.85[ASN][1000 genomes]
rs2492405	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2492407	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2492408	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2492409	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2492410	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2492411	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2492412	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2493648	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2819026	0.81[AMR][1000 genomes]
rs2819032	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819033	0.81[EUR][1000 genomes]
rs2819034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2946992	0.88[ASN][1000 genomes]
rs2999276	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2999282	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2999286	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2999287	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3000700	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4559639	0.81[AMR][1000 genomes]
rs4584528	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4597022	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4948726	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56059584	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60739384	0.88[ASN][1000 genomes]
rs61859002	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6421744	0.80[AFR][1000 genomes]
rs7069214	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7070029	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7088430	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7089290	0.81[AMR][1000 genomes]
rs7092125	0.80[EUR][1000 genomes]
rs7092599	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7894374	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7905676	0.99[ASN][1000 genomes]
rs9422371	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv825355	chr10:43890579-43923802	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv825356	chr10:43893080-43946515	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43892200-43896600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:43893000-43897000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:43893200-43898400	Genic enhancers	Hela-S3	cervix
4	chr10:43893200-43901600	Weak transcription	HSMMtube	muscle
5	chr10:43893400-43899800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
6	chr10:43893400-43901400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr10:43893600-43897000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr10:43893600-43899000	Enhancers	HUVEC	blood vessel
9	chr10:43893600-43899800	Genic enhancers	NHEK	skin
10	chr10:43893600-43901200	Weak transcription	Brain Angular Gyrus	brain
11	chr10:43893600-43902200	Weak transcription	Aorta	Aorta
12	chr10:43893800-43897400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr10:43893800-43897400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr10:43893800-43897400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
15	chr10:43893800-43898400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr10:43893800-43898800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:43893800-43899000	Weak transcription	Brain Substantia Nigra	brain
18	chr10:43894000-43899400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:43894000-43899800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr10:43894000-43901200	Weak transcription	Brain Hippocampus Middle	brain
21	chr10:43894000-43901200	Genic enhancers	Fetal Intestine Small	intestine
22	chr10:43894000-43901400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:43894200-43897400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:43894200-43899200	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr10:43894200-43899200	Transcr. at gene 5' and 3'	K562	blood
26	chr10:43894200-43901200	Weak transcription	Brain Anterior Caudate	brain
27	chr10:43894200-43901400	Weak transcription	Fetal Brain Male	brain
28	chr10:43894400-43897400	Genic enhancers	NHLF	lung
29	chr10:43894400-43898800	Genic enhancers	HMEC	breast
30	chr10:43894400-43899800	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr10:43894400-43900200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr10:43894400-43901200	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr10:43894400-43901200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr10:43894400-43901600	Weak transcription	Brain Germinal Matrix	brain
35	chr10:43894600-43896600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
36	chr10:43894800-43896800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
37	chr10:43894800-43896800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
38	chr10:43894800-43896800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr10:43894800-43899800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr10:43894800-43899800	Genic enhancers	Monocytes-CD14+_RO01746	blood
41	chr10:43894800-43901400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr10:43894800-43901600	Weak transcription	Fetal Brain Female	brain
43	chr10:43895000-43896600	Weak transcription	Ovary	ovary
44	chr10:43895000-43897200	Weak transcription	Esophagus	oesophagus
45	chr10:43895000-43897400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr10:43895000-43898400	Weak transcription	Colonic Mucosa	Colon
47	chr10:43895000-43898400	Weak transcription	Fetal Stomach	stomach
48	chr10:43895000-43898600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr10:43895000-43898600	Weak transcription	Right Atrium	heart
50	chr10:43895000-43899000	Genic enhancers	NHDF-Ad	bronchial

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