Variant report

Variant	rs28561965
Chromosome Location	chr14:69441422-69441423
allele	C/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	CTCF	chr14:69441340-69441490	GM12872	blood:	n/a	n/a
2	CHD1	chr14:69441180-69450261	IMR90	lung:	n/a	chr14:69446695-69446705
3	POLR2A	chr14:69441361-69441676	HepG2	liver:	n/a	n/a
4	POLR2A	chr14:69441212-69441522	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr14:69441293-69442157	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr14:69441221-69441611	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr14:69441170-69441768	U87	brain:	n/a	n/a
8	POLR2A	chr14:69441251-69441502	HepG2	liver:	n/a	n/a
9	POLR2A	chr14:69441290-69449923	IMR90	lung:	n/a	n/a
10	POLR2A	chr14:69441164-69443163	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:69377936..69380482-chr14:69440340..69442074,2	MCF-7	breast:
2	chr14:69402982..69422523-chr14:69436263..69448017,46	MCF-7	breast:

Variant related genes	Relation type
ACTN1-AS1	TF binding region
ENSG00000072110	Chromatin interaction
ENSG00000258531	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1007407	0.96[ASN][1000 genomes]
rs10137547	1.00[ASN][1000 genomes]
rs10139165	0.93[EUR][1000 genomes]
rs10143111	0.89[AFR][1000 genomes]
rs10147976	1.00[ASN][1000 genomes]
rs11627719	0.93[AMR][1000 genomes]
rs11628549	0.95[EUR][1000 genomes]
rs11628773	0.93[EUR][1000 genomes]
rs12432970	0.90[ASN][1000 genomes]
rs12434478	0.90[ASN][1000 genomes]
rs17093668	0.86[ASN][1000 genomes]
rs17106670	0.90[ASN][1000 genomes]
rs2012750	1.00[ASN][1000 genomes]
rs2012764	1.00[ASN][1000 genomes]
rs2012785	1.00[ASN][1000 genomes]
rs2024892	0.86[ASN][1000 genomes]
rs2024893	0.86[ASN][1000 genomes]
rs2268968	0.86[ASN][1000 genomes]
rs2300875	1.00[ASN][1000 genomes]
rs28396849	0.83[AFR][1000 genomes]
rs4243632	0.96[ASN][1000 genomes]
rs4902682	0.90[ASN][1000 genomes]
rs7149487	0.90[ASN][1000 genomes]
rs72733548	0.86[ASN][1000 genomes]
rs8009158	0.86[AFR][1000 genomes]
rs8016537	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69411200-69442600	Weak transcription	Fetal Brain Female	brain
2	chr14:69420600-69441600	Genic enhancers	NH-A	brain
3	chr14:69421200-69442200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr14:69428400-69442200	Genic enhancers	Fetal Stomach	stomach
5	chr14:69428600-69443400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:69429400-69443800	Weak transcription	Brain Germinal Matrix	brain
7	chr14:69429800-69442400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr14:69430000-69441600	Genic enhancers	HSMM	muscle
9	chr14:69431800-69444000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
10	chr14:69432000-69442400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:69432600-69442200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr14:69432600-69443000	Weak transcription	Brain Substantia Nigra	brain
13	chr14:69433200-69442000	Genic enhancers	Muscle Satellite Cultured Cells	--
14	chr14:69434200-69441600	Weak transcription	Ovary	ovary
15	chr14:69434400-69442400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr14:69435600-69441600	Genic enhancers	HMEC	breast
17	chr14:69436200-69442600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr14:69436400-69441800	Weak transcription	Brain Angular Gyrus	brain
19	chr14:69436600-69442000	Weak transcription	Brain Hippocampus Middle	brain
20	chr14:69437000-69443000	Weak transcription	Fetal Brain Male	brain
21	chr14:69437200-69442000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr14:69437400-69441800	Genic enhancers	A549	lung
23	chr14:69437400-69441800	Genic enhancers	Osteobl	bone
24	chr14:69437400-69442200	Genic enhancers	HUVEC	blood vessel
25	chr14:69437600-69441600	Strong transcription	Fetal Muscle Leg	muscle
26	chr14:69437600-69441800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr14:69437800-69441600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr14:69437800-69443600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr14:69438000-69441600	Genic enhancers	Liver	Liver
30	chr14:69438200-69442400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:69438200-69442600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr14:69438200-69442600	Weak transcription	Fetal Kidney	kidney
33	chr14:69438200-69443200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr14:69438400-69441600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr14:69438400-69442200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr14:69438400-69444400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr14:69438600-69442000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr14:69438600-69443000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr14:69438800-69441800	Strong transcription	Dnd41	blood
40	chr14:69438800-69442800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr14:69438800-69443000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr14:69438800-69443400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr14:69438800-69444000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr14:69439000-69443600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr14:69439200-69441600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr14:69439200-69441600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr14:69439200-69442000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr14:69439200-69442200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr14:69439200-69444400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
50	chr14:69439400-69442800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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