Variant report

Variant	rs7898026
Chromosome Location	chr10:49497934-49497935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:226)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:226 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr10:49497800-49497950	GM12871	blood:	n/a	n/a
2	RAD21	chr10:49497690-49498032	A549	lung:	n/a	n/a
3	RAD21	chr10:49497623-49498136	MCF-7	breast:	n/a	n/a
4	CTCF	chr10:49497800-49497950	GM12865	blood:	n/a	n/a
5	CTCF	chr10:49497820-49497970	GM12872	blood:	n/a	n/a
6	CTCF	chr10:49497800-49497950	AG09309	skin:	n/a	n/a
7	USF1	chr10:49497731-49498005	SK-N-SH_RA	brain:	n/a	n/a
8	CTCF	chr10:49497820-49497970	GM12873	blood:	n/a	n/a
9	MAZ	chr10:49497713-49497965	GM12878	blood:	n/a	n/a
10	CTCF	chr10:49497744-49498005	MCF-7	breast:	n/a	n/a
11	CTCF	chr10:49497698-49498138	MCF-7	breast:	n/a	n/a
12	CTCF	chr10:49497740-49498022	ProgFib	skin:	n/a	n/a
13	CTCF	chr10:49497691-49498012	ECC-1	luminal epithelium:	n/a	n/a
14	MAX	chr10:49497669-49498011	GM12878	blood:	n/a	n/a
15	RAD21	chr10:49497707-49497955	K562	blood:	n/a	n/a
16	CTCF	chr10:49497820-49497970	Caco-2	colon:	n/a	n/a
17	CEBPB	chr10:49497290-49498112	GM12878	blood:	n/a	chr10:49497431-49497443
18	CTCF	chr10:49497674-49497985	A549	lung:	n/a	n/a
19	CTCF	chr10:49497840-49497990	HEK293	kidney:	n/a	n/a
20	ATF2	chr10:49497607-49498044	H1-hESC	embryonic stem cell:	n/a	n/a
21	SMC3	chr10:49497602-49498072	Hela-S3	cervix:	n/a	chr10:49497881-49497889
22	CTCF	chr10:49497800-49497950	GM12875	blood:	n/a	n/a
23	CTCF	chr10:49497820-49497970	GM12878	blood:	n/a	n/a
24	RAD21	chr10:49497656-49498028	GM12878	blood:	n/a	n/a
25	CTCF	chr10:49497840-49497990	GM12867	blood:	n/a	n/a
26	CTCF	chr10:49497737-49498029	NHEK	skin:	n/a	n/a
27	SMC3	chr10:49497693-49498079	HepG2	liver:	n/a	chr10:49497881-49497889
28	ZNF143	chr10:49497651-49498055	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr10:49497723-49498036	GM12878	blood:	n/a	n/a
30	CTCF	chr10:49497800-49497950	HAc	cerebellar:	n/a	n/a
31	RAD21	chr10:49497670-49498059	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr10:49497728-49498042	GM12892	blood:	n/a	n/a
33	CTCF	chr10:49497800-49497950	GM12873	blood:	n/a	n/a
34	CTCF	chr10:49497765-49498026	HepG2	liver:	n/a	n/a
35	RAD21	chr10:49497501-49498218	HCT-116	colon:	n/a	n/a
36	RAD21	chr10:49497701-49498019	GM12878	blood:	n/a	n/a
37	CEBPB	chr10:49497781-49498022	K562	blood:	n/a	n/a
38	RAD21	chr10:49497691-49498052	HepG2	liver:	n/a	n/a
39	ZNF143	chr10:49497671-49498067	GM12878	blood:	n/a	n/a
40	CTCF	chr10:49497730-49498034	Gliobla	brain:	n/a	n/a
41	CTCF	chr10:49497800-49497950	GM12864	blood:	n/a	n/a
42	CTCF	chr10:49497696-49498027	ECC-1	luminal epithelium:	n/a	n/a
43	CTCF	chr10:49497749-49498038	Medullo	brain:	n/a	n/a
44	RAD21	chr10:49497630-49498060	GM12878	blood:	n/a	n/a
45	EP300	chr10:49497646-49497990	K562	blood:	n/a	n/a
46	RAD21	chr10:49497699-49498061	HepG2	liver:	n/a	n/a
47	CTCF	chr10:49497820-49497970	NHEK	skin:	n/a	n/a
48	CTCF	chr10:49497625-49498096	T-47D	breast:	n/a	n/a
49	USF1	chr10:49497764-49498060	K562	blood:	n/a	n/a
50	CTCF	chr10:49497754-49497999	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:49423127..49424126-chr10:49497102..49498218,5	MCF-7	breast:
2	chr10:49496582..49501262-chr10:49513244..49517429,4	K562	blood:
3	chr10:49423481..49424232-chr10:49497847..49498349,2	K562	blood:
4	chr10:49489462..49491590-chr10:49496144..49498930,2	MCF-7	breast:
5	chr10:49423144..49424160-chr10:49497116..49498379,10	MCF-7	breast:
6	chr10:49497874..49500351-chr10:49502359..49504964,2	MCF-7	breast:
7	chr10:49422440..49425186-chr10:49494550..49500073,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225482	TF binding region
ENSG00000107643	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10508903	0.80[CHB][hapmap]
rs10745265	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10776590	0.80[ASN][1000 genomes]
rs10776591	0.86[ASN][1000 genomes]
rs10776592	0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10776593	0.83[ASN][1000 genomes]
rs10776594	0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10776595	0.80[CHB][hapmap]
rs10776596	0.80[CHB][hapmap]
rs10857554	0.86[ASN][1000 genomes]
rs10857560	0.80[CHB][hapmap]
rs10857564	0.94[JPT][hapmap]
rs10857565	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs11101280	0.80[ASN][1000 genomes]
rs11101282	0.86[ASN][1000 genomes]
rs11101285	0.94[JPT][hapmap]
rs11101318	0.80[CHB][hapmap]
rs11101320	0.80[CHB][hapmap]
rs1112268	0.83[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11597435	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs11598320	0.88[JPT][hapmap]
rs12358297	0.94[JPT][hapmap]
rs17780725	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs1881735	0.82[CHD][hapmap];0.94[JPT][hapmap]
rs1881737	0.94[JPT][hapmap]
rs1881740	0.83[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1881741	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs1919706	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1919707	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1919709	0.83[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1919710	0.80[ASN][1000 genomes]
rs1919712	0.80[CHB][hapmap]
rs1997365	1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2178339	0.81[ASN][1000 genomes]
rs2377140	0.82[ASN][1000 genomes]
rs2377141	0.87[ASN][1000 genomes]
rs2377142	0.85[ASN][1000 genomes]
rs2377143	0.94[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs2377349	0.83[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs2590386	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2590391	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2698758	0.94[JPT][hapmap]
rs2698768	0.94[JPT][hapmap]
rs2889595	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs3827680	0.80[CHB][hapmap]
rs4012930	0.86[ASN][1000 genomes]
rs4529852	0.85[ASN][1000 genomes]
rs4838404	0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4838405	0.83[ASN][1000 genomes]
rs4838588	0.81[ASN][1000 genomes]
rs4838590	0.80[CHB][hapmap]
rs6537559	1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6537561	0.80[CHB][hapmap]
rs7068398	0.88[JPT][hapmap]
rs7072515	0.80[CHB][hapmap]
rs7075976	0.80[CHB][hapmap]
rs7086275	0.80[CHB][hapmap]
rs7095392	0.86[ASN][1000 genomes]
rs7097975	0.93[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7101060	0.80[CHB][hapmap]
rs9284	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550812	chr10:49484698-49524715	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7898026	FRMPD2	cis	parietal	SCAN
rs7898026	ANTXRL	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49492400-49498200	Enhancers	Fetal Thymus	thymus
2	chr10:49493200-49499800	Enhancers	GM12878-XiMat	blood
3	chr10:49493600-49504200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:49494400-49498000	Weak transcription	Adipose Nuclei	Adipose
5	chr10:49495000-49498000	Enhancers	Brain Hippocampus Middle	brain
6	chr10:49495200-49498200	Enhancers	Brain Substantia Nigra	brain
7	chr10:49495400-49498200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr10:49495400-49498800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr10:49495400-49500400	Enhancers	Placenta	Placenta
10	chr10:49495600-49498200	Enhancers	Brain Anterior Caudate	brain
11	chr10:49495600-49498800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr10:49495800-49498200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr10:49495800-49500400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr10:49496200-49498000	Weak transcription	Fetal Muscle Leg	muscle
15	chr10:49496400-49498000	Weak transcription	Brain Germinal Matrix	brain
16	chr10:49496400-49498800	Weak transcription	Gastric	stomach
17	chr10:49496400-49514200	Weak transcription	Right Atrium	heart
18	chr10:49496800-49501800	Enhancers	Dnd41	blood
19	chr10:49497000-49498000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr10:49497000-49499800	Enhancers	HepG2	liver
21	chr10:49497200-49498000	Weak transcription	Pancreas	Pancrea
22	chr10:49497200-49498200	Enhancers	Brain Angular Gyrus	brain
23	chr10:49497200-49498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr10:49497200-49499200	Enhancers	Duodenum Mucosa	Duodenum
25	chr10:49497400-49498000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:49497400-49498000	Enhancers	Esophagus	oesophagus
27	chr10:49497400-49498200	Enhancers	Colon Smooth Muscle	Colon
28	chr10:49497400-49498600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr10:49497400-49499800	Enhancers	Fetal Intestine Large	intestine
30	chr10:49497600-49498200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
31	chr10:49497600-49498200	Enhancers	H9 Cell Line	embryonic stem cell
32	chr10:49497600-49498200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:49497600-49498200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr10:49497600-49498200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr10:49497600-49498200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr10:49497600-49498200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr10:49497600-49498200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr10:49497600-49498200	Enhancers	Fetal Brain Male	brain
39	chr10:49497600-49498200	Enhancers	Stomach Mucosa	stomach
40	chr10:49497600-49498200	Enhancers	A549	lung
41	chr10:49497600-49500000	Enhancers	Fetal Intestine Small	intestine
42	chr10:49497600-49500000	Enhancers	K562	blood
43	chr10:49497800-49498000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr10:49497800-49498200	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr10:49497800-49499000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr10:49497800-49499000	Weak transcription	NH-A	brain

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