Variant report

Variant	rs4838598
Chromosome Location	chr10:49679413-49679414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:64)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:64 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr10:49678889-49679749	K562	blood:	n/a	n/a
2	POLR2A	chr10:49676024-49679787	K562	blood:	n/a	n/a
3	POLR2A	chr10:49677023-49679444	K562	blood:	n/a	n/a
4	MAX	chr10:49678110-49679689	K562	blood:	n/a	n/a
5	TBL1XR1	chr10:49678172-49679720	K562	blood:	n/a	n/a
6	POLR2A	chr10:49679413-49679677	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr10:49679367-49679776	MCF10A-Er-Src	breast:	n/a	n/a
8	ZNF384	chr10:49677940-49679483	K562	blood:	n/a	n/a
9	CTCF	chr10:49679095-49679522	K562	blood:	n/a	n/a
10	FOS	chr10:49679372-49679760	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr10:49679320-49679470	A549	lung:	n/a	n/a
12	CTCF	chr10:49679320-49679470	NHEK	skin:	n/a	n/a
13	CTCF	chr10:49679280-49679430	HMEC	breast:	n/a	n/a
14	EP300	chr10:49677951-49679790	K562	blood:	n/a	n/a
15	POLR2A	chr10:49676135-49679814	K562	blood:	n/a	n/a
16	CBX3	chr10:49678932-49679960	K562	blood:	n/a	n/a
17	BHLHE40	chr10:49679261-49679734	K562	blood:	n/a	n/a
18	IRF1	chr10:49678101-49679858	K562	blood:	n/a	chr10:49679312-49679326
19	CTCF	chr10:49679220-49679470	GM12871	blood:	n/a	n/a
20	ZMIZ1	chr10:49678054-49679506	K562	blood:	n/a	n/a
21	CTCF	chr10:49679400-49679550	HBMEC	blood vessel:	n/a	n/a
22	CTCF	chr10:49679400-49679550	HMF	breast:	n/a	n/a
23	UBTF	chr10:49679168-49679517	K562	blood:	n/a	n/a
24	CTCF	chr10:49679400-49679550	AG04450	lung:	n/a	n/a
25	MAFK	chr10:49677359-49679863	K562	blood:	n/a	n/a
26	HCFC1	chr10:49679154-49679557	K562	blood:	n/a	n/a
27	POLR2A	chr10:49675855-49679748	K562	blood:	n/a	n/a
28	CUX1	chr10:49679301-49679873	K562	blood:	n/a	n/a
29	CTCF	chr10:49679400-49679550	AG09309	skin:	n/a	n/a
30	JUND	chr10:49677370-49679695	K562	blood:	n/a	chr10:49678975-49678987
31	FOS	chr10:49679367-49679777	MCF10A-Er-Src	breast:	n/a	n/a
32	MAFK	chr10:49679348-49679717	IMR90	lung:	n/a	n/a
33	POLR2A	chr10:49679110-49679885	U87	brain:	n/a	n/a
34	YY1	chr10:49679200-49679480	K562	blood:	n/a	n/a
35	GATA1	chr10:49676752-49680318	K562	blood:	n/a	chr10:49678382-49678389 chr10:49678473-49678483 chr10:49678138-49678154 chr10:49678138-49678154
36	MYC	chr10:49679089-49679442	K562	blood:	n/a	n/a
37	CEBPB	chr10:49679286-49679551	K562	blood:	n/a	n/a
38	CTCF	chr10:49679300-49679450	AG04450	lung:	n/a	n/a
39	CTCF	chr10:49679220-49679510	HCT-116	colon:	n/a	n/a
40	RCOR1	chr10:49677151-49679904	K562	blood:	n/a	n/a
41	ZNF143	chr10:49678884-49679489	K562	blood:	n/a	chr10:49679133-49679142
42	POLR2A	chr10:49678996-49679573	K562	blood:	n/a	n/a
43	POLR2A	chr10:49679240-49679681	U87	brain:	n/a	n/a
44	MYC	chr10:49679171-49679727	K562	blood:	n/a	n/a
45	MYC	chr10:49679395-49679718	MCF10A-Er-Src	breast:	n/a	n/a
46	MAZ	chr10:49677952-49679865	K562	blood:	n/a	n/a
47	CTCF	chr10:49679280-49679430	HEK293	kidney:	n/a	n/a
48	POLR2A	chr10:49677307-49679553	K562	blood:	n/a	n/a
49	CTCF	chr10:49679380-49679530	MCF-7	breast:	n/a	n/a
50	CTCF	chr10:49679311-49679499	IMR90	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr10:49679191..49679816-chr10:49714272..49714777,2	K562	blood:
2	chr10:49646827..49648798-chr10:49677849..49680976,3	K562	blood:
3	chr10:49620234..49623060-chr10:49677590..49681287,3	K562	blood:
4	chr10:49677142..49679992-chr10:49728038..49732327,4	K562	blood:
5	chr10:49677417..49680316-chr10:49708989..49711504,2	K562	blood:
6	chr10:49602827..49604920-chr10:49676681..49679745,3	K562	blood:
7	chr10:49640741..49644596-chr10:49677175..49679458,3	K562	blood:

No data

Variant related genes	Relation type
ARHGAP22	TF binding region
ENSG00000128805	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10857574	0.83[ASN][1000 genomes]
rs11101326	0.90[JPT][hapmap]
rs11101328	0.81[ASN][1000 genomes]
rs11101330	0.83[EUR][1000 genomes]
rs11101331	0.87[ASN][1000 genomes]
rs11101333	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11101336	0.85[ASN][1000 genomes]
rs11101340	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598657	0.80[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1867579	0.95[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2377354	0.89[CHB][hapmap];1.00[CHD][hapmap]
rs3844600	0.85[CHB][hapmap]
rs3853762	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3954044	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4838594	0.84[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4838596	0.82[JPT][hapmap]
rs4838597	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs730509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9794032	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv467191	chr10:49669142-49735563	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv550813	chr10:49669142-49735563	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4838598	ANTXRL	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49671000-49680400	Enhancers	Primary hematopoietic stem cells	blood
2	chr10:49672400-49683400	Weak transcription	Spleen	Spleen
3	chr10:49672600-49681800	Weak transcription	Aorta	Aorta
4	chr10:49673000-49681200	Weak transcription	HSMM	muscle
5	chr10:49675000-49679800	Enhancers	Fetal Thymus	thymus
6	chr10:49675200-49680000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr10:49675200-49680000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:49675600-49679800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr10:49676000-49679800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr10:49676000-49680200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:49676200-49679600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:49676200-49679600	Enhancers	Ovary	ovary
13	chr10:49676200-49679800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr10:49676200-49681600	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr10:49676800-49680000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:49676800-49680200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:49676800-49680400	Enhancers	NHEK	skin
18	chr10:49677000-49680800	Enhancers	HMEC	breast
19	chr10:49677200-49680200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:49677400-49679600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr10:49677400-49679800	Enhancers	Brain Hippocampus Middle	brain
22	chr10:49677400-49680000	Enhancers	Esophagus	oesophagus
23	chr10:49677600-49679600	Enhancers	Brain Angular Gyrus	brain
24	chr10:49677600-49679800	Enhancers	Brain Substantia Nigra	brain
25	chr10:49677600-49679800	Enhancers	HUVEC	blood vessel
26	chr10:49677800-49679800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr10:49678200-49679800	Enhancers	NH-A	brain
28	chr10:49678200-49687200	Weak transcription	HSMMtube	muscle
29	chr10:49678400-49681000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:49678400-49683800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr10:49678800-49680000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr10:49678800-49684000	Weak transcription	Placenta	Placenta
33	chr10:49678800-49684200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr10:49678800-49684200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr10:49678800-49684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:49678800-49684200	Weak transcription	Right Atrium	heart
37	chr10:49679000-49680000	Enhancers	Osteobl	bone
38	chr10:49679000-49683800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr10:49679000-49683800	Weak transcription	Fetal Stomach	stomach
40	chr10:49679000-49684200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr10:49679000-49684400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr10:49679200-49679600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr10:49679200-49679800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr10:49679200-49680400	Genic enhancers	K562	blood
45	chr10:49679200-49682000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr10:49679200-49690400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr10:49679400-49679600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr10:49679400-49679800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr10:49679400-49679800	Enhancers	NHDF-Ad	bronchial
50	chr10:49679400-49679800	Genic enhancers	NHLF	lung

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