Variant report

Variant	rs10254562
Chromosome Location	chr7:39661524-39661525
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:91)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:91 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU2F2	chr7:39661284-39661928	GM12878	blood:	n/a	n/a
2	IRF1	chr7:39661342-39661930	K562	blood:	n/a	n/a
3	SPI1	chr7:39661389-39661552	K562	blood:	n/a	chr7:39661459-39661472
4	SPI1	chr7:39661255-39661793	HL-60	blood:	n/a	chr7:39661459-39661472
5	EP300	chr7:39661324-39661802	GM12878	blood:	n/a	n/a
6	SPI1	chr7:39661290-39661630	GM12878	blood:	n/a	chr7:39661459-39661472
7	NFIC	chr7:39661229-39661813	GM12878	blood:	n/a	n/a
8	TCF12	chr7:39660530-39661691	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr7:39661358-39663450	K562	blood:	n/a	n/a
10	POLR2A	chr7:39661360-39663434	K562	blood:	n/a	n/a
11	POLR2A	chr7:39661305-39661870	U87	brain:	n/a	n/a
12	TEAD4	chr7:39661278-39662101	K562	blood:	n/a	n/a
13	CEBPB	chr7:39661313-39662192	K562	blood:	n/a	n/a
14	MAZ	chr7:39661439-39662037	GM12878	blood:	n/a	n/a
15	POLR2A	chr7:39659839-39663493	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr7:39660809-39665213	IMR90	lung:	n/a	n/a
17	BHLHE40	chr7:39661523-39661683	K562	blood:	n/a	n/a
18	SPI1	chr7:39661362-39661595	K562	blood:	n/a	chr7:39661459-39661472
19	POLR2A	chr7:39661347-39661899	GM12892	blood:	n/a	n/a
20	CHD2	chr7:39661403-39661707	GM12878	blood:	n/a	n/a
21	RUNX3	chr7:39661293-39661681	GM12878	blood:	n/a	n/a
22	POLR2A	chr7:39661268-39663897	GM12878	blood:	n/a	n/a
23	PML	chr7:39661219-39661829	GM12878	blood:	n/a	n/a
24	FOXM1	chr7:39661243-39661680	GM12878	blood:	n/a	n/a
25	ZNF384	chr7:39661503-39661705	GM12878	blood:	n/a	n/a
26	TBL1XR1	chr7:39661478-39661858	K562	blood:	n/a	n/a
27	POLR2A	chr7:39661250-39663630	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr7:39661378-39661695	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr7:39661454-39661793	GM12891	blood:	n/a	n/a
30	CHD1	chr7:39661323-39661886	GM12878	blood:	n/a	n/a
31	MTA3	chr7:39661297-39661914	GM12878	blood:	n/a	n/a
32	NFATC1	chr7:39661269-39661750	GM12878	blood:	n/a	n/a
33	MAZ	chr7:39661407-39664395	K562	blood:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
34	MYC	chr7:39661436-39661952	K562	blood:	n/a	n/a
35	POLR2A	chr7:39661351-39664265	HepG2	liver:	n/a	n/a
36	POLR2A	chr7:39661469-39661546	ProgFib	skin:	n/a	n/a
37	NFYB	chr7:39661392-39661879	GM12878	blood:	n/a	n/a
38	RCOR1	chr7:39661453-39661726	GM12878	blood:	n/a	n/a
39	RFX5	chr7:39661470-39661967	GM12878	blood:	n/a	chr7:39661789-39661804 chr7:39661807-39661822
40	POLR2A	chr7:39661394-39663507	GM12878	blood:	n/a	n/a
41	STAT1	chr7:39661405-39661557	GM12878	blood:	n/a	n/a
42	TBL1XR1	chr7:39661431-39662064	K562	blood:	n/a	n/a
43	ATF2	chr7:39661234-39661741	GM12878	blood:	n/a	n/a
44	JUND	chr7:39661325-39665588	K562	blood:	n/a	chr7:39664844-39664855 chr7:39664121-39664130 chr7:39663142-39663151 chr7:39663137-39663146
45	ATF1	chr7:39661316-39661776	K562	blood:	n/a	n/a
46	POLR2A	chr7:39661367-39663802	GM18505	blood:	n/a	n/a
47	POLR2A	chr7:39661392-39664433	GM12878	blood:	n/a	n/a
48	SPI1	chr7:39661292-39661759	GM12891	blood:	n/a	chr7:39661459-39661472
49	SPI1	chr7:39661337-39661593	GM12878	blood:	n/a	chr7:39661459-39661472
50	POLR2A	chr7:39661434-39663828	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:39616830..39619300-chr7:39660316..39662885,2	K562	blood:
2	chr7:39652942..39654975-chr7:39661144..39662912,2	MCF-7	breast:
3	chr7:39655737..39658310-chr7:39659914..39661763,2	MCF-7	breast:
4	chr7:39645097..39647250-chr7:39658816..39661772,2	MCF-7	breast:
5	chr7:39661404..39663086-chr7:39725958..39728030,2	MCF-7	breast:
6	chr7:39660516..39662861-chr7:39772033..39774524,2	K562	blood:
7	chr17:56735362..56737542-chr7:39660335..39663097,2	MCF-7	breast:
8	chr7:39661332..39663000-chr7:39732479..39734683,2	K562	blood:
9	chr7:39660619..39666370-chr7:39771379..39777121,13	MCF-7	breast:
10	chr7:39635256..39637997-chr7:39660350..39662905,2	MCF-7	breast:
11	chr7:39643128..39644638-chr7:39660434..39662671,2	MCF-7	breast:
12	chr7:39661063..39664836-chr7:39769831..39775766,6	MCF-7	breast:
13	chr7:39660450..39662052-chr7:39725858..39728733,2	K562	blood:
14	chr7:39660345..39662229-chr7:39666445..39668711,2	MCF-7	breast:

No data

Variant related genes	Relation type
RALA	TF binding region
ENSG00000006451	Chromatin interaction
ENSG00000188185	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10232064	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11769865	0.80[MEX][hapmap]
rs11769962	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11769987	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11982634	0.80[MEX][hapmap]
rs13224312	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2008819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2158547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35694450	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4723888	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6462938	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6462939	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6948088	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7806633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7806769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10254562	RALA	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39645200-39661600	Weak transcription	A549	lung
2	chr7:39655200-39661800	Weak transcription	Pancreas	Pancrea
3	chr7:39656600-39661800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:39657000-39662200	Weak transcription	HUVEC	blood vessel
5	chr7:39658000-39662400	Weak transcription	Esophagus	oesophagus
6	chr7:39658600-39661800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:39658600-39661800	Weak transcription	Fetal Lung	lung
8	chr7:39659000-39661600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:39659200-39661800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:39659400-39661600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:39659400-39661800	Weak transcription	Fetal Thymus	thymus
12	chr7:39659400-39661800	Enhancers	HSMM	muscle
13	chr7:39659400-39662200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:39659600-39662200	Enhancers	HMEC	breast
15	chr7:39659800-39661600	Enhancers	NHLF	lung
16	chr7:39659800-39661800	Enhancers	HSMMtube	muscle
17	chr7:39659800-39662000	Enhancers	Osteobl	bone
18	chr7:39659800-39662200	Enhancers	NHDF-Ad	bronchial
19	chr7:39660000-39661800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr7:39660000-39662000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:39660200-39661600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:39660400-39661600	Enhancers	GM12878-XiMat	blood
23	chr7:39660400-39661600	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr7:39660400-39662400	Enhancers	Primary hematopoietic stem cells	blood
25	chr7:39660600-39661600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:39660600-39662200	Enhancers	Primary B cells from cord blood	blood
27	chr7:39660600-39662200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:39661000-39661600	Enhancers	Spleen	Spleen
29	chr7:39661000-39661600	Enhancers	K562	blood
30	chr7:39661000-39661800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:39661000-39662000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr7:39661000-39662400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr7:39661000-39662400	Enhancers	Primary B cells from peripheral blood	blood
34	chr7:39661200-39662000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:39661200-39662400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr7:39661200-39662600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:39661200-39662800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr7:39661400-39661600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:39661400-39661600	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr7:39661400-39661600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:39661400-39661600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:39661400-39661600	Enhancers	Aorta	Aorta
43	chr7:39661400-39661600	Enhancers	Dnd41	blood
44	chr7:39661400-39661800	Enhancers	H9 Cell Line	embryonic stem cell
45	chr7:39661400-39661800	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr7:39661400-39661800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:39661400-39661800	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr7:39661400-39661800	Enhancers	HepG2	liver
49	chr7:39661400-39662000	Enhancers	Primary T cells from cord blood	blood
50	chr7:39661400-39662000	Enhancers	Skeletal Muscle Male	skeletal muscle

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