Variant report

Variant	rs17610725
Chromosome Location	chr4:48864595-48864596
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	POLR2A	chr4:48862350-48865447	K562	blood:	n/a	n/a
2	POLR2A	chr4:48864082-48865009	HCT-116	colon:	n/a	n/a
3	POLR2A	chr4:48863964-48864657	H1-hESC	embryonic stem cell:	n/a	n/a
4	MTA3	chr4:48864037-48864737	GM12878	blood:	n/a	n/a
5	EBF1	chr4:48864396-48864650	GM12878	blood:	n/a	chr4:48864528-48864539
6	NFATC1	chr4:48864507-48865116	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:48864020-48864652	MCF-7	breast:	n/a	n/a
8	POLR2A	chr4:48864125-48864665	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr4:48863971-48865376	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr4:48863494-48865316	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:48847293..48849915-chr4:48863724..48865303,2	MCF-7	breast:
2	chr4:48783503..48785645-chr4:48863021..48865080,2	MCF-7	breast:
3	chr4:48862851..48865784-chr4:48884723..48887077,2	MCF-7	breast:
4	chr4:48853189..48856829-chr4:48863048..48867064,3	K562	blood:

Variant related genes	Relation type
OCIAD1-AS1	TF binding region
ENSG00000109180	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10938546	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12509766	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap]
rs1517675	1.00[CHB][hapmap]
rs17656727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656763	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824039	0.85[EUR][1000 genomes]
rs1824040	0.85[EUR][1000 genomes]
rs2304387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354947	1.00[ASN][1000 genomes]
rs2354948	1.00[ASN][1000 genomes]
rs45463191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62310925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447674	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73815372	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746513	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48834000-48864600	Weak transcription	Stomach Mucosa	stomach
2	chr4:48838200-48866800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:48841000-48865400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:48848200-48864600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:48848200-48864600	Weak transcription	Fetal Heart	heart
6	chr4:48848200-48880000	Weak transcription	Brain Substantia Nigra	brain
7	chr4:48854400-48864800	Weak transcription	HSMMtube	muscle
8	chr4:48854400-48865800	Weak transcription	Brain Angular Gyrus	brain
9	chr4:48856400-48865600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:48856800-48864600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:48857000-48866000	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:48860200-48865200	Weak transcription	Lung	lung
13	chr4:48860400-48864600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:48860400-48882200	Weak transcription	Gastric	stomach
15	chr4:48860400-48901400	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:48860600-48864800	Weak transcription	Right Ventricle	heart
17	chr4:48860600-48865200	Weak transcription	NHLF	lung
18	chr4:48860600-48868600	Weak transcription	Fetal Kidney	kidney
19	chr4:48860600-48872600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:48860600-48873600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:48860800-48864600	Weak transcription	NHEK	skin
22	chr4:48860800-48865000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:48860800-48865200	Weak transcription	Fetal Intestine Small	intestine
24	chr4:48860800-48865200	Weak transcription	Fetal Stomach	stomach
25	chr4:48860800-48865400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:48860800-48865600	Weak transcription	Fetal Brain Female	brain
27	chr4:48860800-48865600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:48860800-48871800	Weak transcription	Ovary	ovary
29	chr4:48860800-48871800	Weak transcription	Pancreas	Pancrea
30	chr4:48860800-48872000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:48860800-48872400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:48860800-48873000	Weak transcription	Primary T cells from cord blood	blood
33	chr4:48860800-48892000	Weak transcription	Thymus	Thymus
34	chr4:48860800-48892800	Weak transcription	Aorta	Aorta
35	chr4:48860800-48892800	Weak transcription	Left Ventricle	heart
36	chr4:48860800-48895000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:48860800-48895000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:48861600-48865600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:48862400-48864600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:48862400-48865200	Weak transcription	Fetal Thymus	thymus
41	chr4:48862800-48864600	Weak transcription	HUVEC	blood vessel
42	chr4:48862800-48866600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:48863000-48864600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:48863000-48865000	Weak transcription	NH-A	brain
45	chr4:48863000-48865400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:48863000-48865600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr4:48863000-48865800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:48863000-48865800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr4:48863000-48866400	Weak transcription	HMEC	breast
50	chr4:48863200-48864800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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