Variant report

Variant	rs10201856
Chromosome Location	chr2:99767419-99767420
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	STAT3	chr2:99767182-99767460	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr2:99767173-99767483	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr2:99767082-99767478	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr2:99767253-99767529	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr2:99767228-99767472	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:99767143-99767579	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr2:99767212-99767529	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr2:99767232-99767554	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr2:99767249-99767608	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr2:99767190-99767575	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:99767297..99778137-chr2:99793643..99800044,16	MCF-7	breast:
2	chr2:99762915..99768009-chr2:99769933..99773290,6	K562	blood:
3	chr2:99767233..99772869-chr2:99793831..99799744,8	K562	blood:
4	chr2:99763174..99765422-chr2:99765700..99768337,2	K562	blood:
5	chr2:99766752..99769279-chr2:99800257..99802967,2	MCF-7	breast:
6	chr2:99761230..99762915-chr2:99766513..99769061,2	K562	blood:

Variant related genes	Relation type
ENSG00000273155	TF binding region
LIPT1	TF binding region
ENSG00000135951	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000241962	Chromatin interaction
ENSG00000185414	Chromatin interaction
ENSG00000144182	Chromatin interaction
ENSG00000273155	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10176788	0.88[AFR][1000 genomes]
rs12475034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13009147	0.82[CHB][hapmap]
rs13428547	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17760953	0.82[CHB][hapmap]
rs4622780	0.84[CHB][hapmap]
rs7591519	1.00[YRI][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv535839	chr2:99742621-99793747	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99758600-99770200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:99758600-99770400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:99758600-99770400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:99758600-99770600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:99758600-99770600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:99758800-99769600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:99758800-99770000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr2:99758800-99770200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:99758800-99770200	Weak transcription	Fetal Brain Female	brain
10	chr2:99758800-99770400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:99758800-99770600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:99759000-99767600	Weak transcription	Primary B cells from cord blood	blood
13	chr2:99759000-99769000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:99759000-99769400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:99759000-99769400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:99759000-99769600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:99759000-99769600	Weak transcription	Brain Angular Gyrus	brain
18	chr2:99759000-99769600	Weak transcription	Thymus	Thymus
19	chr2:99759000-99769800	Weak transcription	Primary T cells from cord blood	blood
20	chr2:99759000-99770200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:99759000-99770200	Weak transcription	HMEC	breast
22	chr2:99759000-99770400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:99759000-99770400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:99759000-99770400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:99759000-99770400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr2:99759000-99770400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:99759000-99770400	Weak transcription	Brain Anterior Caudate	brain
28	chr2:99759000-99770600	Weak transcription	Fetal Kidney	kidney
29	chr2:99759200-99769600	Weak transcription	Hela-S3	cervix
30	chr2:99759200-99770400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:99759200-99770400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:99759200-99770400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:99759200-99770400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:99759400-99769200	Weak transcription	HepG2	liver
35	chr2:99763400-99770400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr2:99764600-99770000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:99764600-99770400	Weak transcription	Psoas Muscle	Psoas
38	chr2:99765800-99769400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:99766000-99768200	Weak transcription	Fetal Intestine Small	intestine
40	chr2:99766600-99768200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:99767000-99767600	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr2:99767000-99767800	Strong transcription	Fetal Intestine Large	intestine
43	chr2:99767000-99768200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr2:99767200-99767800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:99767200-99769600	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links