Variant report

Variant	rs1258044
Chromosome Location	chr1:47016512-47016513
allele	A/G
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	E2F6	chr1:47016407-47016865	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr1:47016332-47016796	H1-hESC	embryonic stem cell:	n/a	chr1:47016718-47016729

No.	Distal block	Cell Line	Cell type
1	chr1:47015863..47022104-chr1:47022936..47029939,8	K562	blood:
2	chr1:47012476..47015757-chr1:47016043..47020828,4	K562	blood:
3	chr1:47012476..47015680-chr1:47016269..47019098,3	K562	blood:

Variant related genes	Relation type
KNCN	TF binding region
ENSG00000079277	Chromatin interaction
ENSG00000162456	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10890403	0.94[ASN][1000 genomes]
rs10890404	0.95[ASN][1000 genomes]
rs11801320	0.93[ASN][1000 genomes]
rs12142727	0.89[EUR][1000 genomes]
rs12145313	0.87[EUR][1000 genomes]
rs1258030	0.89[EUR][1000 genomes]
rs1258031	0.83[EUR][1000 genomes]
rs1258032	0.86[EUR][1000 genomes]
rs1258033	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1258034	0.88[EUR][1000 genomes]
rs1258035	0.90[EUR][1000 genomes]
rs1258043	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1258049	0.97[ASN][1000 genomes]
rs1923810	0.88[EUR][1000 genomes]
rs4660356	0.89[EUR][1000 genomes]
rs61395024	0.86[ASN][1000 genomes]
rs7523809	0.92[ASN][1000 genomes]
rs8602	0.89[ASN][1000 genomes]
rs885127	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription 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 target site	32 gene(s)	inside rSNPs	diseases
4	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv998422	chr1:46969626-47023671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv534953	chr1:46969626-47023671	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1009899	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv534954	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv1011892	chr1:47010519-47067492	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46999600-47035000	Weak transcription	Right Atrium	heart
2	chr1:47013800-47022000	Weak transcription	HMEC	breast
3	chr1:47014000-47026600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:47014200-47016800	Enhancers	Fetal Brain Male	brain
5	chr1:47014400-47016800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:47015000-47016600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:47015000-47016600	Enhancers	Brain Germinal Matrix	brain
8	chr1:47015000-47016800	Bivalent Enhancer	Fetal Stomach	stomach
9	chr1:47015000-47019000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr1:47015200-47016600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:47015200-47017600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:47015400-47016600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr1:47015400-47016600	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr1:47015400-47016600	Enhancers	K562	blood
15	chr1:47015400-47016800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
16	chr1:47015400-47017000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:47015400-47017000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:47015400-47024600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:47015600-47016600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr1:47015600-47017600	Weak transcription	Esophagus	oesophagus
21	chr1:47015600-47024000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:47015600-47024200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:47015600-47025800	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:47015800-47016600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:47015800-47016800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:47015800-47023400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:47015800-47023800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:47015800-47023800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:47015800-47024600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:47015800-47026200	Weak transcription	Primary B cells from cord blood	blood
31	chr1:47015800-47041200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:47015800-47043400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:47016000-47016600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:47016000-47016600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
35	chr1:47016000-47020000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:47016000-47023200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:47016000-47025200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:47016000-47025600	Weak transcription	Fetal Brain Female	brain
39	chr1:47016000-47027000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:47016000-47037400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:47016200-47016800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr1:47016200-47026000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr1:47016200-47030400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:47016400-47016600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:47016400-47023600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:47016400-47025600	Weak transcription	Brain Anterior Caudate	brain

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