Variant report

Variant	rs2463948
Chromosome Location	chr10:57391147-57391148
allele	A/C
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	chr10:57391060-57391210	HCPEpiC	choroid plexus:	n/a	chr10:57391108-57391121
2	CTCF	chr10:57391002-57391336	MCF-7	breast:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
3	JUND	chr10:57390866-57391334	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr10:57391080-57391230	AG10803	skin:	n/a	chr10:57391216-57391229 chr10:57391108-57391121
5	POLR2A	chr10:57390772-57391468	H1-hESC	embryonic stem cell:	n/a	n/a
6	GABPA	chr10:57390705-57391434	MCF-7	breast:	n/a	n/a
7	CTCF	chr10:57391120-57391270	SAEC	small airway:	n/a	chr10:57391216-57391229 chr10:57391240-57391248
8	TAF1	chr10:57390772-57391448	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr10:57391006-57391358	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr10:57390909-57391367	MCF-7	breast:	n/a	n/a
11	CTCF	chr10:57391080-57391230	SK-N-SH_RA	brain:	n/a	chr10:57391216-57391229 chr10:57391108-57391121
12	CTCF	chr10:57391120-57391270	GM12864	blood:	n/a	chr10:57391216-57391229 chr10:57391240-57391248
13	RAD21	chr10:57391006-57391220	K562	blood:	n/a	n/a
14	CTCF	chr10:57391080-57391230	HMEC	breast:	n/a	chr10:57391216-57391229 chr10:57391108-57391121
15	CTCF	chr10:57391080-57391230	GM12875	blood:	n/a	chr10:57391216-57391229 chr10:57391108-57391121
16	CTCF	chr10:57391060-57391210	HBMEC	blood vessel:	n/a	chr10:57391108-57391121
17	CTCF	chr10:57391080-57391230	NHEK	skin:	n/a	chr10:57391216-57391229 chr10:57391108-57391121
18	CTCF	chr10:57391080-57391230	HEK293	kidney:	n/a	chr10:57391216-57391229 chr10:57391108-57391121
19	CTCF	chr10:57391120-57391270	HA-sp	spinal cord:	n/a	chr10:57391216-57391229 chr10:57391240-57391248
20	REST	chr10:57390699-57391710	H1-neurons	neurons:	n/a	chr10:57390870-57390880
21	CTCF	chr10:57391120-57391270	HFF-Myc	foreskin:	n/a	chr10:57391216-57391229 chr10:57391240-57391248
22	RAD21	chr10:57390942-57391290	HepG2	liver:	n/a	chr10:57391215-57391229
23	MYC	chr10:57391073-57391326	MCF-7	breast:	n/a	n/a
24	CTCF	chr10:57391028-57391320	GM19238	blood:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
25	POLR2A	chr10:57390875-57391416	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr10:57391004-57391356	MCF-7	breast:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
27	CTCF	chr10:57391066-57391280	Kidney_OC	kidney:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
28	SIN3A	chr10:57390708-57391550	H1-hESC	embryonic stem cell:	n/a	chr10:57390871-57390880
29	CTCF	chr10:57390907-57391374	H1-hESC	embryonic stem cell:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
30	CTCF	chr10:57391080-57391230	HepG2	liver:	n/a	chr10:57391216-57391229 chr10:57391108-57391121
31	E2F6	chr10:57390755-57391300	H1-hESC	embryonic stem cell:	n/a	n/a
32	E2F6	chr10:57390728-57391272	A549	lung:	n/a	n/a
33	TAF1	chr10:57390817-57391405	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr10:57391100-57391250	HPAF	blood vessel:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
35	YY1	chr10:57390855-57391163	GM12878	blood:	n/a	n/a
36	CTCF	chr10:57391100-57391250	GM12871	blood:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
37	CTCF	chr10:57391060-57391210	HFF-Myc	foreskin:	n/a	chr10:57391108-57391121
38	CTCF	chr10:57391065-57391245	GM13976	blood:	n/a	chr10:57391216-57391229 chr10:57391108-57391121
39	CTCF	chr10:57390976-57391337	A549	lung:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
40	CTCF	chr10:57390916-57391473	MCF-7	breast:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
41	RAD21	chr10:57390884-57391306	MCF-7	breast:	n/a	chr10:57391215-57391229
42	CTCF	chr10:57391080-57391230	A549	lung:	n/a	chr10:57391216-57391229 chr10:57391108-57391121
43	CTCF	chr10:57391052-57391290	LNCaP	prostate:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
44	CTCF	chr10:57390998-57391343	A549	lung:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
45	CTCF	chr10:57391040-57391190	GM12867	blood:	n/a	chr10:57391108-57391121
46	CTCF	chr10:57391072-57391344	HepG2	liver:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
47	CTCF	chr10:57391080-57391230	NHDF-neo	bronchial:	n/a	chr10:57391216-57391229 chr10:57391108-57391121
48	CTCF	chr10:57390794-57391624	A549	lung:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57391240-57391248
49	BACH1	chr10:57390168-57391406	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr10:57391080-57391230	HL-60	blood:	n/a	chr10:57391216-57391229 chr10:57391108-57391121

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:57046815..57047629-chr10:57390561..57391169,3	MCF-7	breast:

Variant related genes	Relation type
PCDH15	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10430549	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10465984	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10763215	0.82[EUR][1000 genomes]
rs10763219	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10825549	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11004891	0.82[EUR][1000 genomes]
rs12264767	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1413665	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1916524	0.88[EUR][1000 genomes]
rs2140399	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2184371	0.82[EUR][1000 genomes]
rs2256659	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2257031	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2262189	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2461903	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2461906	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2463946	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2463947	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4642984	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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
22	nsv895490	chr10:57390762-57506658	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:57389400-57391600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr10:57389600-57391200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr10:57389600-57391200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr10:57389600-57391200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
5	chr10:57389600-57391400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:57389600-57391400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr10:57389600-57391400	Active TSS	Fetal Heart	heart
8	chr10:57389600-57391400	Bivalent/Poised TSS	Left Ventricle	heart
9	chr10:57389600-57391400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
10	chr10:57389600-57391600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:57389600-57391600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr10:57389600-57391600	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr10:57389600-57391600	Active TSS	Right Atrium	heart
14	chr10:57389600-57391600	Active TSS	Right Ventricle	heart
15	chr10:57389800-57391400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr10:57389800-57391400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
17	chr10:57389800-57391400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
18	chr10:57389800-57391400	Active TSS	NHDF-Ad	bronchial
19	chr10:57390000-57391200	Active TSS	Gastric	stomach
20	chr10:57390000-57391400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr10:57390000-57391400	Active TSS	Brain Angular Gyrus	brain
22	chr10:57390000-57391400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
23	chr10:57390000-57391600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr10:57390000-57391600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
25	chr10:57390200-57391200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:57390200-57391200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:57390200-57391400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr10:57390200-57391400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
29	chr10:57390200-57391400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr10:57390200-57391400	Bivalent/Poised TSS	HSMMtube	muscle
31	chr10:57390200-57391600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
32	chr10:57390400-57391200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:57390400-57391200	Active TSS	Brain Anterior Caudate	brain
34	chr10:57390400-57391200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:57390400-57391400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr10:57390400-57391400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:57390400-57391400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr10:57390400-57391600	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr10:57390400-57391600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
40	chr10:57390400-57391600	Active TSS	Brain Substantia Nigra	brain
41	chr10:57390400-57391600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr10:57390400-57391600	Bivalent/Poised TSS	NH-A	brain
43	chr10:57390600-57391200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr10:57390600-57391200	Bivalent/Poised TSS	Thymus	Thymus
45	chr10:57390600-57391400	Flanking Active TSS	Liver	Liver
46	chr10:57390600-57391400	Active TSS	HSMM	muscle
47	chr10:57390600-57391600	Active TSS	H9 Cell Line	embryonic stem cell
48	chr10:57390600-57391600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr10:57390600-57391600	Flanking Active TSS	Fetal Brain Female	brain
50	chr10:57390600-57391600	Bivalent Enhancer	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links