Variant report

Variant	rs9999793
Chromosome Location	chr4:89926540-89926541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10001420	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033435	0.84[ASN][1000 genomes]
rs10033476	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10433881	0.81[ASN][1000 genomes]
rs11734924	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1246630	0.87[ASN][1000 genomes]
rs1246633	0.87[ASN][1000 genomes]
rs1246638	0.83[ASN][1000 genomes]
rs1246641	0.83[ASN][1000 genomes]
rs12647095	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12649875	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1272570	0.87[ASN][1000 genomes]
rs13105546	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13106968	0.87[ASN][1000 genomes]
rs13133608	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1355836	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1355837	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1398937	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1398938	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398939	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398941	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398943	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1458552	0.83[ASN][1000 genomes]
rs1458553	0.83[ASN][1000 genomes]
rs1458555	0.83[ASN][1000 genomes]
rs1513811	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1513812	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1513823	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1533288	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1533289	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1708659	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1708671	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1708672	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1708673	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1708683	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1795730	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795735	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795737	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795740	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1828735	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1903009	0.83[ASN][1000 genomes]
rs1996139	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2045516	0.83[ASN][1000 genomes]
rs2056013	0.85[ASN][1000 genomes]
rs2102650	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2125410	0.83[ASN][1000 genomes]
rs2446295	0.87[ASN][1000 genomes]
rs2446309	0.83[ASN][1000 genomes]
rs2464511	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464521	0.87[ASN][1000 genomes]
rs2609254	0.87[ASN][1000 genomes]
rs2609263	0.87[ASN][1000 genomes]
rs2609274	0.83[ASN][1000 genomes]
rs2609278	0.83[ASN][1000 genomes]
rs2609281	0.83[ASN][1000 genomes]
rs2670618	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2670619	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670620	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670627	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2670628	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704580	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704585	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704588	0.83[ASN][1000 genomes]
rs2704591	0.83[ASN][1000 genomes]
rs2704592	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704593	0.87[ASN][1000 genomes]
rs2704602	0.83[ASN][1000 genomes]
rs2704603	0.83[ASN][1000 genomes]
rs2704606	0.83[ASN][1000 genomes]
rs28559811	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869965	0.87[ASN][1000 genomes]
rs2869968	0.83[ASN][1000 genomes]
rs2869989	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28718401	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28869547	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904264	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6532100	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6532113	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6823241	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6826482	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6834297	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6845264	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6846010	0.81[ASN][1000 genomes]
rs7657630	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7673427	0.87[ASN][1000 genomes]
rs7697878	0.87[ASN][1000 genomes]
rs8180333	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs922027	0.83[ASN][1000 genomes]
rs9307063	0.81[ASN][1000 genomes]
rs938265	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs938267	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs973680	0.87[ASN][1000 genomes]
rs987314	0.83[ASN][1000 genomes]
rs993358	0.87[ASN][1000 genomes]
rs9999873	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89878400-89927600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:89896800-89934800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr4:89903000-89957200	Weak transcription	HSMM	muscle
4	chr4:89903400-89936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:89904200-89927600	Weak transcription	Pancreas	Pancrea
6	chr4:89906600-89927400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:89907800-89927400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:89908400-89926600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:89908800-89927400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:89909800-89931200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:89910400-89927600	Weak transcription	Ovary	ovary
12	chr4:89911400-89930400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:89911600-89926600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:89912200-89935800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:89912200-89943800	Weak transcription	Psoas Muscle	Psoas
16	chr4:89912400-89927600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:89913400-89930800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:89913400-89944000	Weak transcription	Gastric	stomach
19	chr4:89915800-89927200	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:89917200-89927400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:89919400-89926600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:89920000-89927200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:89920400-89937000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:89921000-89930000	Weak transcription	Liver	Liver
25	chr4:89921000-89950600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:89922000-89927600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:89922400-89936000	Weak transcription	Adipose Nuclei	Adipose
28	chr4:89922600-89926600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:89922600-89927600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:89922600-89932600	Weak transcription	NHDF-Ad	bronchial
31	chr4:89922600-89935000	Weak transcription	Placenta	Placenta
32	chr4:89922600-89936800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:89922600-89949800	Weak transcription	HMEC	breast
34	chr4:89922800-89927600	Weak transcription	HepG2	liver
35	chr4:89922800-89931800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:89922800-89935800	Weak transcription	HUVEC	blood vessel
37	chr4:89922800-89945600	Weak transcription	A549	lung
38	chr4:89923000-89927400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:89923000-89932200	Weak transcription	Osteobl	bone
40	chr4:89923000-89935000	Weak transcription	Fetal Kidney	kidney
41	chr4:89923400-89939400	Weak transcription	Primary T cells from cord blood	blood
42	chr4:89923600-89927600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:89923600-89927600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:89923600-89930800	Weak transcription	Small Intestine	intestine
45	chr4:89923600-89945600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr4:89923800-89927200	Weak transcription	Fetal Intestine Small	intestine
47	chr4:89923800-89927400	Weak transcription	Fetal Intestine Large	intestine
48	chr4:89923800-89927400	Weak transcription	Fetal Stomach	stomach
49	chr4:89923800-89927400	Weak transcription	K562	blood
50	chr4:89923800-89927600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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