Variant report

Variant	rs789986
Chromosome Location	chr4:130015752-130015753
allele	C/G
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	MXI1	chr4:130012946-130016268	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr4:130012893-130015801	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr4:130015548-130015922	K562	blood:	n/a	n/a
4	STAT3	chr4:130015608-130016123	MCF10A-Er-Src	breast:	n/a	n/a
5	IRF1	chr4:130013950-130015756	K562	blood:	n/a	chr4:130015414-130015426 chr4:130014820-130014829 chr4:130015578-130015585 chr4:130014330-130014347 chr4:130015415-130015425 chr4:130014330-130014344 chr4:130015414-130015427
6	ARID3A	chr4:130015591-130017978	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:128703531..128705249-chr4:130014655..130017577,2	K562	blood:
2	chr4:129731090..129733904-chr4:130015000..130016574,3	K562	blood:
3	chr4:129730340..129733748-chr4:130013373..130016609,5	K562	blood:

Variant related genes	Relation type
SCLT1	TF binding region
C4orf33	TF binding region
ENSG00000164070	Chromatin interaction
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10014640	0.85[JPT][hapmap]
rs10028124	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10857134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12650832	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13132428	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1450727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699390	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1699396	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1709416	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1709417	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1757941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs175964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs186444	0.85[JPT][hapmap]
rs1947269	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2167244	0.85[JPT][hapmap]
rs2218814	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2592953	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2592955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs280592	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs280598	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs280600	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs280602	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2893267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3099898	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3119696	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs318512	0.86[JPT][hapmap]
rs318533	0.85[JPT][hapmap]
rs318535	0.84[JPT][hapmap]
rs318537	0.86[JPT][hapmap]
rs318538	0.89[JPT][hapmap]
rs318540	0.90[JPT][hapmap]
rs318542	0.85[JPT][hapmap]
rs318544	0.85[JPT][hapmap]
rs318546	0.85[JPT][hapmap]
rs318547	0.84[JPT][hapmap]
rs318548	0.85[JPT][hapmap]
rs318549	0.85[JPT][hapmap]
rs318554	0.90[JPT][hapmap]
rs318562	0.85[JPT][hapmap]
rs318564	0.86[JPT][hapmap]
rs337264	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4165	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975192	0.90[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975287	0.86[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975288	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975289	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4975290	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975291	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975292	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs498435	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs536631	0.95[CEU][hapmap]
rs62316963	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62318666	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6814109	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6817901	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6820403	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6820637	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6821814	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6830229	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6840358	0.86[JPT][hapmap]
rs7666529	0.85[JPT][hapmap]
rs7668762	0.84[JPT][hapmap]
rs7671455	0.88[AMR][1000 genomes]
rs7691218	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130011200-130016000	Active TSS	NHLF	lung
2	chr4:130011200-130016400	Active TSS	GM12878-XiMat	blood
3	chr4:130012400-130015800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:130012600-130015800	Active TSS	Brain Hippocampus Middle	brain
5	chr4:130012800-130018600	Active TSS	K562	blood
6	chr4:130013400-130015800	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr4:130013600-130015800	Active TSS	Fetal Brain Female	brain
8	chr4:130013600-130016000	Active TSS	Muscle Satellite Cultured Cells	--
9	chr4:130013800-130016200	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr4:130014800-130017200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:130014800-130017200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:130015000-130015800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr4:130015000-130016000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:130015000-130017200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:130015000-130017200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:130015000-130017200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:130015000-130017200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:130015200-130015800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:130015200-130015800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr4:130015200-130015800	Enhancers	Fetal Heart	heart
21	chr4:130015200-130015800	Flanking Active TSS	Fetal Kidney	kidney
22	chr4:130015200-130016200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:130015200-130017000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:130015200-130017000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:130015200-130017000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:130015200-130017200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr4:130015200-130017200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:130015200-130017200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:130015200-130017200	Weak transcription	Esophagus	oesophagus
30	chr4:130015200-130017200	Weak transcription	Placenta	Placenta
31	chr4:130015200-130017200	Weak transcription	Left Ventricle	heart
32	chr4:130015200-130017200	Weak transcription	Lung	lung
33	chr4:130015200-130017200	Weak transcription	Pancreas	Pancrea
34	chr4:130015200-130017200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr4:130015200-130017200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:130015200-130017200	Weak transcription	Small Intestine	intestine
37	chr4:130015200-130017200	Weak transcription	HSMM	muscle
38	chr4:130015200-130017200	Weak transcription	HSMMtube	muscle
39	chr4:130015400-130015800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr4:130015400-130015800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:130015400-130015800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:130015400-130015800	Enhancers	Duodenum Mucosa	Duodenum
43	chr4:130015400-130015800	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr4:130015400-130015800	Flanking Active TSS	HMEC	breast
45	chr4:130015400-130016000	Enhancers	Adipose Nuclei	Adipose
46	chr4:130015400-130016000	Enhancers	Colon Smooth Muscle	Colon
47	chr4:130015400-130016000	Enhancers	NHDF-Ad	bronchial
48	chr4:130015400-130016000	Enhancers	Osteobl	bone
49	chr4:130015400-130016200	Weak transcription	HepG2	liver
50	chr4:130015400-130016400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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