Variant report

Variant	rs3924378
Chromosome Location	chr10:5817872-5817873
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	POLR2A	chr10:5817805-5817955	Gliobla	brain:	n/a	n/a
2	POLR2A	chr10:5817730-5818029	GM12878	blood:	n/a	n/a
3	ELF1	chr10:5817661-5818016	GM12878	blood:	n/a	chr10:5817854-5817865
4	POLR2A	chr10:5817776-5817914	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr10:5817808-5817878	MCF-7	breast:	n/a	n/a
6	SPI1	chr10:5817727-5818040	HL-60	blood:	n/a	chr10:5817853-5817866 chr10:5817854-5817867
7	SPI1	chr10:5817680-5818053	GM12891	blood:	n/a	chr10:5817853-5817866 chr10:5817854-5817867
8	SPI1	chr10:5817761-5817910	GM12878	blood:	n/a	chr10:5817853-5817866 chr10:5817854-5817867
9	POLR2A	chr10:5817749-5817934	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYC	chr10:5817758-5817958	MCF-7	breast:	n/a	n/a
11	SPI1	chr10:5817612-5818087	GM12891	blood:	n/a	chr10:5817853-5817866 chr10:5817677-5817684 chr10:5817854-5817867
12	POLR2A	chr10:5817763-5817921	A549	lung:	n/a	n/a
13	TCF3	chr10:5817635-5817949	GM12878	blood:	n/a	n/a
14	SPI1	chr10:5817594-5818123	HL-60	blood:	n/a	chr10:5817853-5817866 chr10:5817677-5817684 chr10:5817854-5817867
15	POLR2A	chr10:5817697-5817936	Hela-S3	cervix:	n/a	n/a
16	MYC	chr10:5817853-5817881	MCF-7	breast:	n/a	n/a
17	POLR2A	chr10:5817745-5817971	MCF-7	breast:	n/a	n/a
18	POLR2A	chr10:5817757-5817957	A549	lung:	n/a	n/a
19	POLR2A	chr10:5817785-5818016	MCF-7	breast:	n/a	n/a
20	POLR2A	chr10:5817664-5818105	HL-60	blood:	n/a	n/a
21	POLR2A	chr10:5817817-5817987	GM12878	blood:	n/a	n/a
22	POLR2A	chr10:5817691-5817962	K562	blood:	n/a	n/a
23	POLR2A	chr10:5817707-5817941	K562	blood:	n/a	n/a
24	POLR2A	chr10:5817708-5818045	K562	blood:	n/a	n/a
25	POLR2A	chr10:5817721-5818009	GM12878	blood:	n/a	n/a
26	CREB1	chr10:5817589-5817981	GM12878	blood:	n/a	chr10:5817787-5817800

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5816487..5819223-chr10:5854186..5856565,2	MCF-7	breast:
2	chr10:5815026..5819070-chr10:5852954..5857275,5	MCF-7	breast:

Variant related genes	Relation type
NRBF2P5	TF binding region
ENSG00000057608	Chromatin interaction
ENSG00000272764	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11253740	1.00[CEU][hapmap]
rs11254115	0.83[ASN][1000 genomes]
rs11254828	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11254891	1.00[CEU][hapmap]
rs11254898	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11255139	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11255237	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11255288	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12221191	0.85[ASN][1000 genomes]
rs12257412	0.81[ASN][1000 genomes]
rs12263390	1.00[CEU][hapmap]
rs12263869	0.84[ASW][hapmap];1.00[CEU][hapmap]
rs12269174	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs12412199	0.85[ASN][1000 genomes]
rs12571055	0.85[ASN][1000 genomes]
rs12572339	0.81[ASN][1000 genomes]
rs1567708	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2246268	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2275772	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2380197	1.00[CEU][hapmap]
rs2669133	0.85[ASN][1000 genomes]
rs2669139	0.85[ASN][1000 genomes]
rs2797490	0.85[ASN][1000 genomes]
rs2797492	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2797497	0.83[ASN][1000 genomes]
rs34404996	0.82[ASN][1000 genomes]
rs3750636	0.85[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3793708	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3793714	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57103262	0.83[ASN][1000 genomes]
rs57832226	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58502403	0.83[ASN][1000 genomes]
rs59827083	0.83[ASN][1000 genomes]
rs60864347	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7089693	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7893673	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7908235	0.86[JPT][hapmap]
rs8177773	1.00[CEU][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	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv947730	chr10:5817688-5827238	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5762600-5843400	Strong transcription	Dnd41	blood
2	chr10:5762800-5843000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:5768000-5849400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:5781400-5818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:5784800-5818000	Weak transcription	Stomach Mucosa	stomach
6	chr10:5788000-5818000	Strong transcription	Duodenum Mucosa	Duodenum
7	chr10:5796000-5822400	Strong transcription	Fetal Intestine Large	intestine
8	chr10:5797200-5819000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr10:5797400-5847400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr10:5798000-5818200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:5798000-5842800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr10:5798200-5843000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr10:5798600-5818400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr10:5798600-5820200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr10:5798600-5842800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr10:5804800-5818200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:5805000-5843200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:5805200-5819000	Strong transcription	GM12878-XiMat	blood
19	chr10:5805600-5818200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr10:5806000-5818200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr10:5807400-5821800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr10:5808400-5826400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr10:5808800-5825800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr10:5809000-5824400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr10:5810400-5818000	Weak transcription	Brain Angular Gyrus	brain
26	chr10:5810400-5818000	Weak transcription	Brain Anterior Caudate	brain
27	chr10:5810400-5824800	Weak transcription	Ovary	ovary
28	chr10:5811800-5824400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr10:5812000-5823800	Weak transcription	Fetal Kidney	kidney
30	chr10:5812000-5824000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:5812400-5821600	Weak transcription	Brain Germinal Matrix	brain
32	chr10:5813000-5818600	Strong transcription	NHEK	skin
33	chr10:5813000-5818800	Strong transcription	HepG2	liver
34	chr10:5813000-5819200	Strong transcription	K562	blood
35	chr10:5813600-5818400	Strong transcription	Fetal Brain Female	brain
36	chr10:5813800-5818400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr10:5814600-5822600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr10:5814800-5819000	Strong transcription	A549	lung
39	chr10:5815400-5818600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr10:5816000-5820200	Strong transcription	Fetal Intestine Small	intestine
41	chr10:5816200-5818000	Genic enhancers	Spleen	Spleen
42	chr10:5816200-5818200	Genic enhancers	Left Ventricle	heart
43	chr10:5816200-5818400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr10:5816400-5818000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr10:5816400-5818000	Strong transcription	Adipose Nuclei	Adipose
46	chr10:5816400-5818200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr10:5816400-5818400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr10:5816400-5818400	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr10:5816400-5818400	Strong transcription	Hela-S3	cervix
50	chr10:5816400-5818800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links