Variant report

Variant	rs2140399
Chromosome Location	chr10:57390119-57390120
allele	C/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	chr10:57389203-57391556	SK-N-SH	brain:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57389621-57389634 chr10:57391240-57391248
2	RAD21	chr10:57389028-57390218	SK-N-SH	brain:	n/a	n/a
3	SIN3A	chr10:57389479-57390410	H1-hESC	embryonic stem cell:	n/a	n/a
4	RFX5	chr10:57387421-57391674	SK-N-SH	brain:	n/a	chr10:57389894-57389902
5	RFX5	chr10:57389683-57391524	H1-hESC	embryonic stem cell:	n/a	chr10:57389894-57389902
6	SMC3	chr10:57390071-57391602	SK-N-SH	brain:	n/a	n/a
7	KAP1	chr10:57389372-57390616	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:57047149..57047763-chr10:57389634..57390254,2	MCF-7	breast:

Variant related genes	Relation type
PCDH15	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10430549	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10465984	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10763215	0.84[EUR][1000 genomes]
rs10763219	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10825549	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11004891	0.84[EUR][1000 genomes]
rs12264767	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1413665	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1916524	0.90[EUR][1000 genomes]
rs2184371	0.84[EUR][1000 genomes]
rs2256659	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2257031	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2262189	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2461903	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2461906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2463946	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2463947	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2463948	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4642984	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039099	chr10:56984902-57394831	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv540641	chr10:56984902-57394831	Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1040047	chr10:57007182-57979747	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv895480	chr10:57120283-57539172	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1046216	chr10:57132407-57470412	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv2761598	chr10:57143239-57656115	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1040346	chr10:57166917-57410348	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv993479	chr10:57187055-57404999	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv895482	chr10:57213026-57476292	Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1053051	chr10:57252816-57638793	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1053015	chr10:57304437-57467168	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1041500	chr10:57317208-57638793	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv895485	chr10:57323162-57431871	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv895486	chr10:57323162-57476292	Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1048800	chr10:57333479-57430517	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv895487	chr10:57335764-57476292	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv895488	chr10:57345779-57401749	Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv551045	chr10:57351781-57442129	Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv895489	chr10:57354709-57420417	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv1048148	chr10:57359414-57498605	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv428558	chr10:57383256-57524282	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2140399	CSTF2T	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:57388600-57390200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:57389400-57391000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr10:57389400-57391600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr10:57389600-57390200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:57389600-57390200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
6	chr10:57389600-57390200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
7	chr10:57389600-57390200	Enhancers	Pancreas	Pancrea
8	chr10:57389600-57390400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
9	chr10:57389600-57390600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr10:57389600-57390800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:57389600-57390800	Bivalent/Poised TSS	Fetal Kidney	kidney
12	chr10:57389600-57390800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
13	chr10:57389600-57391000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr10:57389600-57391000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr10:57389600-57391000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:57389600-57391200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:57389600-57391200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:57389600-57391200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
19	chr10:57389600-57391400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr10:57389600-57391400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr10:57389600-57391400	Active TSS	Fetal Heart	heart
22	chr10:57389600-57391400	Bivalent/Poised TSS	Left Ventricle	heart
23	chr10:57389600-57391400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
24	chr10:57389600-57391600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr10:57389600-57391600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr10:57389600-57391600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr10:57389600-57391600	Active TSS	Right Atrium	heart
28	chr10:57389600-57391600	Active TSS	Right Ventricle	heart
29	chr10:57389800-57390200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
30	chr10:57389800-57390200	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
31	chr10:57389800-57390200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
32	chr10:57389800-57390200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
33	chr10:57389800-57390200	Enhancers	Lung	lung
34	chr10:57389800-57390200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
35	chr10:57389800-57390200	Bivalent Enhancer	A549	lung
36	chr10:57389800-57390400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
37	chr10:57389800-57390400	Flanking Bivalent TSS/Enh	NH-A	brain
38	chr10:57389800-57390600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
39	chr10:57389800-57390800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr10:57389800-57390800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr10:57389800-57390800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
42	chr10:57389800-57390800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
43	chr10:57389800-57390800	Bivalent Enhancer	Stomach Mucosa	stomach
44	chr10:57389800-57391000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
45	chr10:57389800-57391000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr10:57389800-57391400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
47	chr10:57389800-57391400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
48	chr10:57389800-57391400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
49	chr10:57389800-57391400	Active TSS	NHDF-Ad	bronchial
50	chr10:57390000-57390200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links