Variant report

Variant	rs57625543
Chromosome Location	chr10:98728849-98728850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98718470..98721430-chr10:98726465..98728933,3	MCF-7	breast:
2	chr10:98726233..98732508-chr10:98732953..98737473,8	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11814029	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11815437	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11819015	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17112206	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17112208	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17112234	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17112250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2183447	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28523867	0.89[ASN][1000 genomes]
rs3829856	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4606419	0.86[ASN][1000 genomes]
rs57437078	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57868471	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58550844	0.89[EUR][1000 genomes]
rs72819843	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72819851	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72819853	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72819856	1.00[AFR][1000 genomes]
rs72819857	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72819858	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7911787	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1052931	chr10:98676192-98862301	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS 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 miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1042398	chr10:98691406-98851346	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831951	chr10:98717103-98761280	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98709200-98736200	Weak transcription	Psoas Muscle	Psoas
2	chr10:98712800-98731200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:98715400-98733800	Weak transcription	A549	lung
4	chr10:98715400-98740600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:98715400-98740600	Weak transcription	Aorta	Aorta
6	chr10:98715400-98740600	Weak transcription	Esophagus	oesophagus
7	chr10:98715600-98731000	Weak transcription	Small Intestine	intestine
8	chr10:98715600-98735600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr10:98715600-98740600	Weak transcription	Fetal Stomach	stomach
10	chr10:98715600-98740600	Weak transcription	NHEK	skin
11	chr10:98715800-98740600	Weak transcription	Lung	lung
12	chr10:98716000-98732200	Weak transcription	GM12878-XiMat	blood
13	chr10:98716000-98733600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr10:98716000-98737600	Weak transcription	Thymus	Thymus
15	chr10:98716000-98740200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:98716000-98740400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr10:98716000-98740600	Weak transcription	Brain Anterior Caudate	brain
18	chr10:98716000-98740600	Weak transcription	Gastric	stomach
19	chr10:98716000-98740600	Weak transcription	Left Ventricle	heart
20	chr10:98716000-98740600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr10:98716000-98741000	Weak transcription	Brain Germinal Matrix	brain
22	chr10:98716200-98740800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr10:98716400-98740600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr10:98716600-98739800	Weak transcription	Primary T cells from cord blood	blood
25	chr10:98716600-98740600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr10:98716600-98740600	Weak transcription	Ovary	ovary
27	chr10:98716600-98740600	Weak transcription	HMEC	breast
28	chr10:98716600-98743200	Weak transcription	Hela-S3	cervix
29	chr10:98716800-98733400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:98716800-98740600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr10:98717000-98740600	Weak transcription	Fetal Kidney	kidney
32	chr10:98717400-98740600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr10:98717800-98740600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:98718200-98733800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr10:98718600-98740400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr10:98718600-98740600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr10:98719000-98740600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:98719000-98740600	Weak transcription	Dnd41	blood
39	chr10:98719200-98732000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr10:98719200-98733600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr10:98719800-98740600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr10:98720000-98739200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr10:98720000-98740400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr10:98720000-98740600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr10:98720000-98740600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr10:98720400-98730800	Weak transcription	Fetal Intestine Large	intestine
47	chr10:98720400-98740600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr10:98720800-98741400	Weak transcription	NHLF	lung
49	chr10:98721000-98731200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr10:98721000-98737400	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links