Variant report

Variant	rs1699396
Chromosome Location	chr4:130010603-130010604
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	chr4:130010467-130010659	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:129731737..129733753-chr4:130010586..130013239,2	MCF-7	breast:
2	chr4:130003975..130008687-chr4:130008780..130012075,4	K562	blood:
3	chr4:130009681..130011304-chr4:130014422..130017412,2	K562	blood:

Variant related genes	Relation type
C4orf33	TF binding region
ENSG00000151466	Chromatin interaction
ENSG00000077684	Chromatin interaction
ENSG00000151470	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10028124	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10857134	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12650832	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13132428	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1450727	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1709416	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1709417	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757941	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs175964	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1947269	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2218814	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2592953	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2592955	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592956	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs280592	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs280598	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs280600	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs280602	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2893267	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3099898	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3119696	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4165	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975192	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975287	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975288	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975289	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4975290	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975291	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975292	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs498435	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62316963	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62318666	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6814109	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6817901	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6820403	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6820637	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6821814	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6830229	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7671455	0.88[AMR][1000 genomes]
rs7691218	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs789986	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129985200-130012200	Weak transcription	HSMM	muscle
2	chr4:129985200-130013000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:129985200-130013200	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:129987000-130011600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:129991600-130011800	Weak transcription	Hela-S3	cervix
6	chr4:129991800-130012000	Weak transcription	HUVEC	blood vessel
7	chr4:129992600-130012000	Weak transcription	HepG2	liver
8	chr4:129993000-130012000	Weak transcription	Stomach Mucosa	stomach
9	chr4:129995600-130011400	Weak transcription	A549	lung
10	chr4:129997200-130012000	Weak transcription	NHEK	skin
11	chr4:129999200-130012600	Weak transcription	NH-A	brain
12	chr4:129999400-130011400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:130000200-130011400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:130000400-130013000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:130001400-130011200	Weak transcription	NHLF	lung
16	chr4:130001400-130013000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:130001800-130011200	Weak transcription	Fetal Heart	heart
18	chr4:130001800-130012000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:130001800-130013000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:130002000-130011800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:130002000-130012600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:130002000-130013200	Weak transcription	Brain Angular Gyrus	brain
23	chr4:130002200-130012000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:130002200-130013400	Weak transcription	Placenta	Placenta
25	chr4:130002600-130011400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:130002600-130012200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:130002800-130011800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:130002800-130011800	Weak transcription	Spleen	Spleen
29	chr4:130002800-130012000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:130002800-130012800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:130002800-130013000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr4:130002800-130013000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:130002800-130013000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:130002800-130013000	Weak transcription	Gastric	stomach
35	chr4:130002800-130013000	Weak transcription	Pancreas	Pancrea
36	chr4:130002800-130013000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:130002800-130013000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr4:130002800-130013200	Weak transcription	Aorta	Aorta
39	chr4:130002800-130013800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:130002800-130013800	Weak transcription	Ovary	ovary
41	chr4:130003000-130010800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:130003000-130010800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:130003000-130011400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:130003000-130011800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:130003000-130011800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr4:130003000-130011800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:130003000-130012000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr4:130003000-130012000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:130003000-130012200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:130003000-130012200	Weak transcription	Fetal Stomach	stomach

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