Variant report

Variant	rs17540492
Chromosome Location	chr10:44882473-44882474
allele	G/T
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	CTCF	chr10:44881944-44882727	SK-N-SH	brain:	n/a	chr10:44882177-44882190 chr10:44882177-44882190 chr10:44882176-44882192 chr10:44882175-44882193 chr10:44882178-44882188 chr10:44882170-44882191 chr10:44882181-44882190
2	CTCF	chr10:44882426-44882542	GM12892	blood:	n/a	n/a
3	CTCF	chr10:44882005-44882510	HCT-116	colon:	n/a	chr10:44882177-44882190 chr10:44882177-44882190 chr10:44882176-44882192 chr10:44882175-44882193 chr10:44882178-44882188 chr10:44882170-44882191 chr10:44882181-44882190
4	CTCF	chr10:44882463-44882539	GM19240	blood:	n/a	n/a
5	RAD21	chr10:44882008-44882869	SK-N-SH	brain:	n/a	chr10:44882173-44882192 chr10:44882176-44882189 chr10:44882175-44882187 chr10:44882177-44882191 chr10:44882179-44882188
6	CTBP2	chr10:44882086-44882642	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr10:44882005-44882478	ECC-1	luminal epithelium:	n/a	chr10:44882173-44882192 chr10:44882176-44882189 chr10:44882175-44882187 chr10:44882177-44882191 chr10:44882179-44882188
8	RAD21	chr10:44882002-44882586	HCT-116	colon:	n/a	chr10:44882173-44882192 chr10:44882176-44882189 chr10:44882175-44882187 chr10:44882177-44882191 chr10:44882179-44882188
9	SMC3	chr10:44881831-44882659	SK-N-SH	brain:	n/a	chr10:44882177-44882191 chr10:44882184-44882191
10	CTCF	chr10:44882400-44882550	AG10803	skin:	n/a	n/a
11	CTCF	chr10:44882460-44882536	GM12878	blood:	n/a	n/a
12	CTCF	chr10:44882360-44882510	Caco-2	colon:	n/a	n/a
13	NRF1	chr10:44882035-44882480	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr10:44881749-44882554	GM12878	blood:	n/a	chr10:44882177-44882190 chr10:44882177-44882190 chr10:44882176-44882192 chr10:44882175-44882193 chr10:44882178-44882188 chr10:44882170-44882191 chr10:44882181-44882190
15	CTCF	chr10:44881998-44882504	IMR90	lung:	n/a	chr10:44882177-44882190 chr10:44882177-44882190 chr10:44882176-44882192 chr10:44882175-44882193 chr10:44882178-44882188 chr10:44882170-44882191 chr10:44882181-44882190
16	RAD21	chr10:44881982-44882484	MCF-7	breast:	n/a	chr10:44882173-44882192 chr10:44882176-44882189 chr10:44882175-44882187 chr10:44882177-44882191 chr10:44882179-44882188
17	SMC3	chr10:44881990-44882569	GM12878	blood:	n/a	chr10:44882177-44882191 chr10:44882184-44882191
18	E2F6	chr10:44882092-44882734	H1-hESC	embryonic stem cell:	n/a	chr10:44882270-44882284 chr10:44882273-44882280 chr10:44882273-44882280 chr10:44882269-44882281 chr10:44882273-44882280
19	CTCF	chr10:44881867-44882533	MCF-7	breast:	n/a	chr10:44882177-44882190 chr10:44882177-44882190 chr10:44882176-44882192 chr10:44882175-44882193 chr10:44882178-44882188 chr10:44882170-44882191 chr10:44882181-44882190
20	CTCF	chr10:44882423-44882541	GM10266	blood:	n/a	n/a
21	CTCF	chr10:44882472-44882501	GM13977	blood:	n/a	n/a
22	RAD21	chr10:44882001-44882496	HCT-116	colon:	n/a	chr10:44882173-44882192 chr10:44882176-44882189 chr10:44882175-44882187 chr10:44882177-44882191 chr10:44882179-44882188
23	RAD21	chr10:44881507-44882691	H1-hESC	embryonic stem cell:	n/a	chr10:44882173-44882192 chr10:44882176-44882189 chr10:44882175-44882187 chr10:44882177-44882191 chr10:44882179-44882188
24	CTCF	chr10:44882460-44882610	GM12866	blood:	n/a	n/a
25	BACH1	chr10:44882052-44882506	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr10:44882017-44882651	A549	lung:	n/a	chr10:44882177-44882190 chr10:44882177-44882190 chr10:44882176-44882192 chr10:44882175-44882193 chr10:44882178-44882188 chr10:44882170-44882191 chr10:44882181-44882190
27	CTCF	chr10:44882440-44882590	Caco-2	colon:	n/a	n/a
28	USF2	chr10:44882067-44882636	H1-hESC	embryonic stem cell:	n/a	chr10:44882150-44882166
29	CTCF	chr10:44881855-44882510	K562	blood:	n/a	chr10:44882177-44882190 chr10:44882177-44882190 chr10:44882176-44882192 chr10:44882175-44882193 chr10:44882178-44882188 chr10:44882170-44882191 chr10:44882181-44882190
30	RAD21	chr10:44881907-44882513	MCF-7	breast:	n/a	chr10:44882173-44882192 chr10:44882176-44882189 chr10:44882175-44882187 chr10:44882177-44882191 chr10:44882179-44882188
31	MAX	chr10:44882056-44882754	NB4	blood:	n/a	chr10:44882242-44882251
32	CTCF	chr10:44882449-44882537	GM10248	blood:	n/a	n/a
33	KAP1	chr10:44882319-44882493	U2OS	brain:	n/a	n/a
34	CTCF	chr10:44882461-44882584	GM20000	blood:	n/a	n/a
35	RAD21	chr10:44881394-44882580	H1-hESC	embryonic stem cell:	n/a	chr10:44882173-44882192 chr10:44882176-44882189 chr10:44882175-44882187 chr10:44882177-44882191 chr10:44882179-44882188
36	CTCF	chr10:44882455-44882533	GM19238	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:44166808..44167608-chr10:44882043..44882606,2	MCF-7	breast:
2	chr10:44779480..44780239-chr10:44881943..44882604,2	K562	blood:

Variant related genes	Relation type
CXCL12	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11239031	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11592974	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11594377	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11595460	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17156193	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17880777	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17883887	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2839679	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2839680	0.85[AFR][1000 genomes]
rs2839683	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2839687	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2839689	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2839690	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2839692	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2839695	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2861441	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2861442	0.85[AFR][1000 genomes]
rs4087301	0.95[EUR][1000 genomes]
rs4520554	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4556491	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4556492	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7082547	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7088876	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7092453	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72790853	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72790854	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72790864	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72790866	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72790869	0.92[EUR][1000 genomes]
rs7915848	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7918568	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44879400-44882600	Bivalent Enhancer	Fetal Brain Male	brain
2	chr10:44880200-44882600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr10:44881000-44882600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr10:44881000-44884600	Weak transcription	Psoas Muscle	Psoas
5	chr10:44881000-44884600	Weak transcription	NHDF-Ad	bronchial
6	chr10:44881200-44882600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
7	chr10:44881200-44884200	Weak transcription	Liver	Liver
8	chr10:44881200-44884200	Weak transcription	Right Atrium	heart
9	chr10:44881200-44884400	Weak transcription	Left Ventricle	heart
10	chr10:44881400-44882600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:44881400-44882600	Bivalent Enhancer	Fetal Stomach	stomach
12	chr10:44881600-44882600	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr10:44881800-44882600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr10:44881800-44882600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr10:44882000-44882800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr10:44882000-44884200	Weak transcription	Adipose Nuclei	Adipose
17	chr10:44882200-44882600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:44882200-44882600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr10:44882200-44882600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
20	chr10:44882200-44882600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
21	chr10:44882200-44882600	Enhancers	Ovary	ovary
22	chr10:44882200-44882600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
23	chr10:44882200-44882600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr10:44882200-44882600	Active TSS	HepG2	liver
25	chr10:44882200-44882600	Flanking Active TSS	Osteobl	bone
26	chr10:44882200-44882800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr10:44882200-44882800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
28	chr10:44882400-44882600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
29	chr10:44882400-44882600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:44882400-44882600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
31	chr10:44882400-44882600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr10:44882400-44882600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
33	chr10:44882400-44882600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr10:44882400-44882600	Bivalent Enhancer	Brain Germinal Matrix	brain
35	chr10:44882400-44882600	Bivalent Enhancer	Fetal Intestine Small	intestine
36	chr10:44882400-44882600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr10:44882400-44882600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr10:44882400-44882600	Enhancers	NHLF	lung
39	chr10:44882400-44882800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
40	chr10:44882400-44882800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
41	chr10:44882400-44882800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
42	chr10:44882400-44882800	Bivalent Enhancer	Fetal Brain Female	brain
43	chr10:44882400-44884000	Weak transcription	Fetal Heart	heart
44	chr10:44882400-44884200	Weak transcription	Right Ventricle	heart
45	chr10:44882400-44884800	Weak transcription	Pancreas	Pancrea

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