Variant report

Variant	rs10193625
Chromosome Location	chr2:153314204-153314205
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	chr2:153313880..153316291-chr2:153320825..153322769,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10166703	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs10173398	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10195380	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10432494	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892232	0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11892859	0.94[ASN][1000 genomes]
rs11893683	0.92[ASN][1000 genomes]
rs12614608	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12617686	0.81[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12623070	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068886	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2346204	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2346209	0.83[CEU][hapmap]
rs2881336	0.81[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2881339	0.83[CEU][hapmap]
rs4143274	0.83[CEU][hapmap]
rs4471845	0.80[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4613221	0.97[ASN][1000 genomes]
rs4664585	0.85[GIH][hapmap]
rs4664587	0.81[CEU][hapmap]
rs6434078	0.95[JPT][hapmap]
rs6721741	0.81[JPT][hapmap]
rs6736639	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6737006	0.90[ASN][1000 genomes]
rs7425826	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7590079	0.80[CEU][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9288103	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv875292	chr2:153308471-153357383	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10193625	TCFL5	trans	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153301800-153321000	Weak transcription	Right Atrium	heart
2	chr2:153302400-153321600	Weak transcription	Left Ventricle	heart
3	chr2:153302800-153314800	Weak transcription	Aorta	Aorta
4	chr2:153303400-153322600	Weak transcription	NHLF	lung
5	chr2:153304400-153321800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:153305600-153321800	Weak transcription	Fetal Intestine Small	intestine
7	chr2:153306200-153319800	Weak transcription	Psoas Muscle	Psoas
8	chr2:153306200-153320200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:153309400-153321600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:153309400-153323600	Enhancers	Brain Angular Gyrus	brain
11	chr2:153310400-153317000	Enhancers	Brain Substantia Nigra	brain
12	chr2:153310400-153318400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:153311600-153318600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:153311800-153321600	Weak transcription	Lung	lung
15	chr2:153312000-153315600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:153312000-153315600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:153312000-153317000	Weak transcription	Ovary	ovary
18	chr2:153312000-153318800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:153312000-153320400	Weak transcription	Fetal Brain Male	brain
20	chr2:153312000-153321400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:153312600-153314800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:153312800-153315600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:153313000-153320800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:153313000-153321000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:153313000-153321600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:153313000-153322000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:153313200-153314400	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:153313200-153314400	Weak transcription	HepG2	liver
29	chr2:153313200-153315000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:153313200-153316800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:153313200-153318400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:153313200-153321200	Weak transcription	A549	lung
33	chr2:153313200-153321600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:153313400-153321200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:153313400-153321400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr2:153313800-153314400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:153313800-153319000	Enhancers	Brain Cingulate Gyrus	brain
38	chr2:153313800-153321000	Weak transcription	NHEK	skin
39	chr2:153314000-153314400	Enhancers	Adipose Nuclei	Adipose
40	chr2:153314000-153314800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:153314200-153314400	Enhancers	Brain Anterior Caudate	brain
42	chr2:153314200-153315200	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links