Variant report

Variant	rs17880777
Chromosome Location	chr10:44881202-44881203
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	E2F6	chr10:44880604-44881305	H1-hESC	embryonic stem cell:	n/a	chr10:44880929-44880941 chr10:44881076-44881086
2	MAX	chr10:44879546-44881252	H1-hESC	embryonic stem cell:	n/a	n/a
3	BACH1	chr10:44880796-44881429	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CXCL12	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11239031	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11592974	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11594377	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11595460	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17156193	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17540492	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17883887	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17885289	0.89[AFR][1000 genomes]
rs2839679	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2839680	0.85[AFR][1000 genomes]
rs2839683	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2839686	0.87[AFR][1000 genomes]
rs2839687	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2839689	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2839690	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2839692	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2839695	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2861441	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2861442	0.85[AFR][1000 genomes]
rs4087301	0.93[EUR][1000 genomes]
rs4520554	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4556491	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4556492	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7082547	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7088876	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7092453	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7093481	0.90[AFR][1000 genomes]
rs72790853	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72790854	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72790861	0.90[AFR][1000 genomes]
rs72790862	0.87[AFR][1000 genomes]
rs72790864	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72790866	0.95[EUR][1000 genomes]
rs72790869	0.90[EUR][1000 genomes]
rs7915848	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7918568	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054649	chr10:44848921-44889713	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv550699	chr10:44868257-44882203	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv895090	chr10:44874867-44884959	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv895091	chr10:44875040-44888130	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv895092	chr10:44875166-44884959	Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv895093	chr10:44876461-44884959	Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv895094	chr10:44876499-44884959	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv895095	chr10:44876586-44884959	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv895096	chr10:44876586-44886206	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv895097	chr10:44876586-44888130	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv895098	chr10:44877501-44881202	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	nsv550700	chr10:44878064-44882203	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	nsv895099	chr10:44878114-44884959	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	nsv895100	chr10:44878835-44884959	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
15	esv3375268	chr10:44878846-44883969	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
16	esv3421241	chr10:44879371-44881919	Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44877800-44881400	Active TSS	Fetal Kidney	kidney
2	chr10:44878600-44881600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
3	chr10:44878800-44881800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr10:44879000-44881400	Active TSS	Brain Anterior Caudate	brain
5	chr10:44879000-44882400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr10:44879400-44882600	Bivalent Enhancer	Fetal Brain Male	brain
7	chr10:44879600-44881400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr10:44879600-44881400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr10:44879600-44881400	Bivalent/Poised TSS	Fetal Stomach	stomach
10	chr10:44879600-44881600	Active TSS	Osteobl	bone
11	chr10:44879600-44882400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr10:44879800-44882200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:44880000-44882400	Bivalent/Poised TSS	Fetal Brain Female	brain
14	chr10:44880200-44881800	Bivalent Enhancer	Placenta	Placenta
15	chr10:44880200-44882600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr10:44880400-44881600	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr10:44880400-44881800	Bivalent/Poised TSS	Colonic Mucosa	Colon
18	chr10:44880400-44881800	Bivalent Enhancer	Spleen	Spleen
19	chr10:44880600-44881400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
20	chr10:44880600-44881600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:44880600-44881600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr10:44880800-44881600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr10:44880800-44881600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
24	chr10:44880800-44881800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
25	chr10:44880800-44881800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr10:44880800-44881800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
27	chr10:44880800-44881800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
28	chr10:44880800-44881800	Bivalent Enhancer	Stomach Mucosa	stomach
29	chr10:44881000-44881400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr10:44881000-44881400	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:44881000-44881400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr10:44881000-44881400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
33	chr10:44881000-44881400	Bivalent Enhancer	Esophagus	oesophagus
34	chr10:44881000-44881600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
35	chr10:44881000-44881600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr10:44881000-44881600	Bivalent Enhancer	Fetal Intestine Large	intestine
37	chr10:44881000-44881800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
38	chr10:44881000-44881800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
39	chr10:44881000-44882200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr10:44881000-44882600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr10:44881000-44884600	Weak transcription	Psoas Muscle	Psoas
42	chr10:44881000-44884600	Weak transcription	NHDF-Ad	bronchial
43	chr10:44881200-44881400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr10:44881200-44881400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr10:44881200-44881400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr10:44881200-44881400	Active TSS	Pancreas	Pancrea
47	chr10:44881200-44881400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
48	chr10:44881200-44881400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
49	chr10:44881200-44881600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:44881200-44881600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links