Variant report

Variant	rs12242149
Chromosome Location	chr10:5888313-5888314
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	FOXM1	chr10:5888049-5888552	GM12878	blood:	n/a	n/a
2	GATA2	chr10:5888106-5888468	SH-SY5Y	brain:	n/a	chr10:5888339-5888348
3	STAT3	chr10:5888236-5888489	MCF10A-Er-Src	breast:	n/a	chr10:5888325-5888336
4	MYC	chr10:5888290-5888490	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr10:5888242-5888478	MCF10A-Er-Src	breast:	n/a	chr10:5888325-5888336
6	SMC3	chr10:5888180-5888421	GM12878	blood:	n/a	n/a
7	IRF4	chr10:5888026-5888351	GM12878	blood:	n/a	n/a
8	CUX1	chr10:5888148-5888457	GM12878	blood:	n/a	n/a
9	EBF1	chr10:5888151-5888610	GM12878	blood:	n/a	n/a
10	ZNF143	chr10:5888143-5888509	GM12878	blood:	n/a	n/a
11	ATF2	chr10:5887991-5888533	GM12878	blood:	n/a	n/a
12	NFIC	chr10:5887892-5888713	GM12878	blood:	n/a	n/a
13	RCOR1	chr10:5888138-5888450	GM12878	blood:	n/a	n/a
14	SPI1	chr10:5887911-5888629	GM12878	blood:	n/a	n/a
15	SP1	chr10:5888103-5888423	GM12878	blood:	n/a	chr10:5888393-5888414
16	RELA	chr10:5888043-5888480	GM18951	blood:	n/a	n/a
17	BATF	chr10:5888064-5888456	GM12878	blood:	n/a	n/a
18	RELA	chr10:5887993-5888503	GM19099	blood:	n/a	n/a
19	PAX5	chr10:5888161-5888413	GM12878	blood:	n/a	n/a
20	BATF	chr10:5888145-5888416	GM12878	blood:	n/a	n/a
21	RELA	chr10:5888066-5888600	GM19193	blood:	n/a	n/a
22	STAT5A	chr10:5888099-5888467	GM12878	blood:	n/a	n/a
23	BCLAF1	chr10:5888041-5888445	GM12878	blood:	n/a	n/a
24	ATF2	chr10:5888079-5888517	GM12878	blood:	n/a	n/a
25	CHD2	chr10:5888040-5888407	GM12878	blood:	n/a	n/a
26	RELA	chr10:5887973-5888559	GM12891	blood:	n/a	n/a
27	MXI1	chr10:5888169-5888568	GM12878	blood:	n/a	n/a
28	SPI1	chr10:5888078-5888332	GM12878	blood:	n/a	n/a
29	MTA3	chr10:5888039-5888575	GM12878	blood:	n/a	n/a
30	JUN	chr10:5888126-5888544	HUVEC	blood vessel:	n/a	chr10:5888396-5888405 chr10:5888338-5888346
31	CHD1	chr10:5888196-5888393	GM12878	blood:	n/a	n/a
32	WRNIP1	chr10:5888090-5888383	GM12878	blood:	n/a	n/a
33	GATA3	chr10:5888212-5888472	SH-SY5Y	brain:	n/a	chr10:5888339-5888348
34	EP300	chr10:5888157-5888365	GM12878	blood:	n/a	n/a
35	NFATC1	chr10:5887964-5888563	GM12878	blood:	n/a	n/a
36	RELA	chr10:5888038-5888507	GM15510	blood:	n/a	n/a
37	BCL3	chr10:5888086-5888466	GM12878	blood:	n/a	n/a
38	NFATC1	chr10:5887971-5888607	GM12878	blood:	n/a	n/a
39	FOS	chr10:5888153-5888518	HUVEC	blood vessel:	n/a	chr10:5888336-5888347 chr10:5888396-5888405 chr10:5888338-5888346
40	STAT1	chr10:5888297-5888469	GM12878	blood:	n/a	n/a
41	BCL11A	chr10:5888070-5888508	GM12878	blood:	n/a	n/a
42	ARID3A	chr10:5888296-5888348	HepG2	liver:	n/a	n/a
43	EP300	chr10:5888159-5888445	GM12878	blood:	n/a	n/a
44	FOS	chr10:5888274-5888428	MCF10A-Er-Src	breast:	n/a	chr10:5888336-5888347 chr10:5888396-5888405 chr10:5888338-5888346
45	FOS	chr10:5888205-5888508	MCF10A-Er-Src	breast:	n/a	chr10:5888336-5888347 chr10:5888396-5888405 chr10:5888338-5888346
46	CUX1	chr10:5888234-5888394	K562	blood:	n/a	n/a
47	JUND	chr10:5888254-5888483	HepG2	liver:	n/a	chr10:5888396-5888405 chr10:5888336-5888347 chr10:5888338-5888346
48	SP1	chr10:5888141-5888460	GM12878	blood:	n/a	chr10:5888393-5888414
49	BCL11A	chr10:5888140-5888401	GM12878	blood:	n/a	n/a
50	TBL1XR1	chr10:5888149-5888488	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:5887234..5889271-chr10:5891738..5894895,3	K562	blood:
2	chr10:5860095..5862542-chr10:5886681..5888594,2	MCF-7	breast:
3	chr10:5854620..5857118-chr10:5886149..5888419,4	K562	blood:
4	chr10:5886207..5890565-chr10:5893992..5897304,3	K562	blood:
5	chr10:5887749..5890618-chr10:5895657..5897180,2	K562	blood:
6	chr10:5852473..5857853-chr10:5880942..5888645,8	MCF-7	breast:

Variant related genes	Relation type
GDI2	TF binding region
ENSG00000272764	Chromatin interaction
ENSG00000057608	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11255505	1.00[CEU][hapmap]
rs11255590	1.00[CEU][hapmap]
rs12245162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12258706	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2669131	1.00[GIH][hapmap]
rs7083699	0.85[YRI][hapmap]
rs7088040	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv5654	chr10:5868365-5930634	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv982902	chr10:5872818-5889953	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv3342274	chr10:5875995-5901345	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv1794948	chr10:5880066-5892545	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv1795821	chr10:5880066-5893268	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv1801910	chr10:5881740-5898882	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv1801679	chr10:5883033-5891501	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	esv1793088	chr10:5883308-5892545	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	esv3528067	chr10:5884196-5893994	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	esv3528068	chr10:5884196-5893994	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	esv1802022	chr10:5886149-5891501	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	esv1850053	chr10:5886435-5892515	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	esv3456507	chr10:5887846-5894644	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	esv3516967	chr10:5888296-5894544	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5883200-5897000	Enhancers	Primary B cells from peripheral blood	blood
2	chr10:5883400-5889000	Enhancers	Primary B cells from cord blood	blood
3	chr10:5886200-5889400	Enhancers	Placenta	Placenta
4	chr10:5886400-5888600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:5886600-5888400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr10:5887000-5888800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:5887000-5888800	Enhancers	Fetal Muscle Leg	muscle
8	chr10:5887000-5889400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:5887200-5888400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr10:5887200-5888400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:5887200-5888400	Weak transcription	NHEK	skin
12	chr10:5887200-5889000	Enhancers	GM12878-XiMat	blood
13	chr10:5887600-5888400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr10:5887600-5888800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr10:5887800-5888800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:5888000-5888600	Enhancers	K562	blood
17	chr10:5888000-5888800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:5888000-5888800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr10:5888000-5888800	Enhancers	HUVEC	blood vessel
20	chr10:5888000-5888800	Enhancers	NHDF-Ad	bronchial
21	chr10:5888000-5889200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr10:5888200-5888400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr10:5888200-5888400	Active TSS	Hela-S3	cervix
24	chr10:5888200-5888600	Enhancers	Rectal Smooth Muscle	rectum
25	chr10:5888200-5888600	Flanking Active TSS	HepG2	liver
26	chr10:5888200-5888600	Enhancers	HMEC	breast
27	chr10:5888200-5888800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr10:5888200-5888800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr10:5888200-5888800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr10:5888200-5888800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr10:5888200-5888800	Enhancers	Adipose Nuclei	Adipose
32	chr10:5888200-5888800	Enhancers	Fetal Intestine Small	intestine

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