Variant report

Variant	rs10176955
Chromosome Location	chr2:208888638-208888639
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:208883906..208887647-chr2:208888508..208891752,4	MCF-7	breast:
2	chr2:208883791..208887954-chr2:208888473..208891537,5	MCF-7	breast:
3	chr2:208627808..208629541-chr2:208887379..208889271,2	MCF-7	breast:
4	chr2:208633416..208635575-chr2:208887303..208890126,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212246	Chromatin interaction
ENSG00000163251	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10176821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10192852	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10200490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11893075	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11899909	1.00[AMR][1000 genomes]
rs13383276	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13391113	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs730419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73066727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73066744	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73066746	0.97[AFR][1000 genomes];1.00[AMR][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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208854200-208889400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:208865200-208889000	Weak transcription	Brain Substantia Nigra	brain
3	chr2:208866600-208889000	Weak transcription	Fetal Stomach	stomach
4	chr2:208866600-208889600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:208866800-208889400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:208867400-208889000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr2:208867400-208889200	Weak transcription	Primary T cells from cord blood	blood
8	chr2:208871800-208889000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:208871800-208889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:208875600-208889000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:208878600-208889600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:208878800-208889000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:208879000-208889400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:208879000-208889400	Weak transcription	Fetal Kidney	kidney
15	chr2:208879200-208889000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:208879400-208889800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:208879600-208889200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:208880000-208889000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:208880600-208889000	Weak transcription	HepG2	liver
20	chr2:208881200-208889600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:208882400-208889600	Weak transcription	Fetal Thymus	thymus
22	chr2:208882600-208889400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:208882600-208889600	Weak transcription	Small Intestine	intestine
24	chr2:208882800-208889000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:208882800-208889400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:208882800-208889400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:208882800-208889600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:208882800-208889600	Weak transcription	Aorta	Aorta
29	chr2:208883400-208889000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:208883600-208889000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:208883600-208889600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:208883800-208889200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:208883800-208889400	Weak transcription	Fetal Intestine Small	intestine
34	chr2:208883800-208889600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:208884200-208889200	Weak transcription	Fetal Intestine Large	intestine
36	chr2:208885200-208889600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:208885400-208888800	Weak transcription	Primary B cells from cord blood	blood
38	chr2:208885600-208889000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:208885600-208889400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr2:208887200-208889000	Enhancers	Brain Angular Gyrus	brain
41	chr2:208887200-208889000	Enhancers	Fetal Brain Female	brain
42	chr2:208887400-208889000	Enhancers	Brain Cingulate Gyrus	brain
43	chr2:208887600-208889600	Weak transcription	Stomach Mucosa	stomach
44	chr2:208887800-208888800	Enhancers	Right Ventricle	heart
45	chr2:208887800-208888800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:208888000-208888800	Enhancers	Lung	lung
47	chr2:208888000-208889000	Enhancers	Fetal Brain Male	brain
48	chr2:208888000-208889200	Enhancers	Adipose Nuclei	Adipose
49	chr2:208888200-208888800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:208888200-208888800	Enhancers	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links