Variant report

Variant	rs10000140
Chromosome Location	chr4:89948054-89948055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10024807	0.87[AMR][1000 genomes]
rs10027874	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029662	0.86[AMR][1000 genomes]
rs10030342	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097209	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11097210	0.87[CEU][hapmap];0.86[AMR][1000 genomes]
rs11097211	0.87[CEU][hapmap];0.86[AMR][1000 genomes]
rs11734085	1.00[ASN][1000 genomes]
rs12506327	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507819	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113298	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs13115669	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120109	1.00[ASN][1000 genomes]
rs13137443	1.00[ASN][1000 genomes]
rs13138946	0.84[EUR][1000 genomes]
rs13140085	0.87[CEU][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs13150503	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513817	1.00[ASN][1000 genomes]
rs1588730	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014988	0.86[AMR][1000 genomes]
rs17770341	1.00[ASN][1000 genomes]
rs17821540	1.00[ASN][1000 genomes]
rs17823587	1.00[ASN][1000 genomes]
rs2056012	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195755	1.00[ASN][1000 genomes]
rs33998578	1.00[ASN][1000 genomes]
rs34008667	1.00[ASN][1000 genomes]
rs34075854	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34300408	1.00[ASN][1000 genomes]
rs34624010	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35130975	0.86[EUR][1000 genomes]
rs35652620	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35909707	1.00[ASN][1000 genomes]
rs36111123	1.00[ASN][1000 genomes]
rs5004788	1.00[ASN][1000 genomes]
rs59385067	0.87[AMR][1000 genomes]
rs61286299	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs62306389	1.00[ASN][1000 genomes]
rs62308627	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532102	0.87[AMR][1000 genomes]
rs6814023	1.00[ASN][1000 genomes]
rs6823660	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826407	0.87[CEU][hapmap];0.85[AMR][1000 genomes]
rs6827398	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6853075	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6856010	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857969	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7660377	0.87[AMR][1000 genomes]
rs7668782	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674344	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs874147	0.87[AMR][1000 genomes]
rs9992522	0.87[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9993181	0.83[YRI][hapmap]
rs9996559	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	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
6	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
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89903000-89957200	Weak transcription	HSMM	muscle
2	chr4:89921000-89950600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:89922600-89949800	Weak transcription	HMEC	breast
4	chr4:89926400-89949600	Weak transcription	Left Ventricle	heart
5	chr4:89926800-89951400	Weak transcription	Right Ventricle	heart
6	chr4:89933600-89951400	Weak transcription	NHLF	lung
7	chr4:89937200-89975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:89938200-89953000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:89939600-89951200	Weak transcription	NHEK	skin
10	chr4:89940200-89949800	Weak transcription	Primary T cells from cord blood	blood
11	chr4:89940200-89957800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:89940400-89956600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:89940400-89956600	Weak transcription	NH-A	brain
14	chr4:89940400-89957800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:89940400-89957800	Weak transcription	Aorta	Aorta
16	chr4:89940400-89959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:89940400-89961000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:89940600-89954400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:89940600-89956000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:89940600-89956000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:89940600-89957800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:89940600-89957800	Weak transcription	Ovary	ovary
23	chr4:89940800-89956800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:89941200-89956000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:89941200-89956200	Weak transcription	Fetal Lung	lung
26	chr4:89941800-89952200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:89941800-89952400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:89941800-89952600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:89941800-89957800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:89941800-89957800	Weak transcription	Fetal Stomach	stomach
31	chr4:89942000-89948600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr4:89942000-89950000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:89942000-89951200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:89942200-89949200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:89943200-89950600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr4:89944200-89951000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:89944200-89954000	Weak transcription	Small Intestine	intestine
38	chr4:89944200-89958000	Weak transcription	Fetal Heart	heart
39	chr4:89944200-89978000	Weak transcription	Pancreas	Pancrea
40	chr4:89944800-89955400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:89945000-89948600	Weak transcription	Fetal Intestine Large	intestine
42	chr4:89945200-89948400	Weak transcription	Fetal Intestine Small	intestine
43	chr4:89945600-89949200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:89945600-89957400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:89945600-89963000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:89945800-89949600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr4:89946200-89972800	Weak transcription	A549	lung
48	chr4:89946400-89950600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:89947400-89948200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:89947800-89948800	Strong transcription	Fetal Muscle Leg	muscle

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