Variant report

Variant	rs10000538
Chromosome Location	chr4:101942483-101942484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10000451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015787	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358312	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1358313	0.92[ASN][1000 genomes]
rs17124	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2037773	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28488364	0.84[ASN][1000 genomes]
rs34422081	0.84[ASN][1000 genomes]
rs3804350	0.81[TSI][hapmap]
rs41498549	0.84[ASN][1000 genomes]
rs58656951	0.84[ASN][1000 genomes]
rs59659135	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850799	0.92[ASN][1000 genomes]
rs6851231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7840	0.84[ASN][1000 genomes]
rs952506	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9684543	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10000538	METAP1	cis	cerebellum	SCAN
rs10000538	MANBA	cis	parietal	SCAN
rs10000538	BANK1	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:101931200-101958000	Weak transcription	Ovary	ovary
2	chr4:101936200-101967800	Weak transcription	Fetal Kidney	kidney
3	chr4:101937200-101943200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:101937400-101943400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr4:101938200-101943400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr4:101940000-101943000	Enhancers	Primary hematopoietic stem cells	blood
7	chr4:101940000-101943000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr4:101940000-101943600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr4:101940200-101942600	Enhancers	Dnd41	blood
10	chr4:101940200-101943000	Enhancers	Primary T cells from cord blood	blood
11	chr4:101940200-101943000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr4:101940200-101943000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr4:101940200-101943200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr4:101940200-101943400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:101940200-101943800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr4:101940200-101943800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:101940200-101944000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr4:101940200-101944000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:101940200-101944200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr4:101940400-101943200	Enhancers	HSMMtube	muscle
21	chr4:101940400-101944000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr4:101940600-101942800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr4:101940600-101943400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr4:101940600-101943600	Weak transcription	Primary B cells from cord blood	blood
25	chr4:101940600-101943600	Enhancers	HMEC	breast
26	chr4:101940600-101943800	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr4:101940600-101944000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:101940800-101943400	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr4:101940800-101943800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr4:101940800-101943800	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:101940800-101943800	Weak transcription	Pancreas	Pancrea
32	chr4:101940800-101944000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:101940800-101958200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:101941000-101943400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr4:101941000-101943600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:101941000-101943800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:101941000-101943800	Weak transcription	Fetal Intestine Large	intestine
38	chr4:101941000-101944000	Enhancers	NH-A	brain
39	chr4:101941000-101960200	Weak transcription	Colonic Mucosa	Colon
40	chr4:101941200-101971000	Weak transcription	Psoas Muscle	Psoas
41	chr4:101941200-102000200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:101941200-102035600	Weak transcription	Fetal Intestine Small	intestine
43	chr4:101941400-101942600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:101941400-101943000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:101941600-101943000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr4:101941600-101959400	Weak transcription	HepG2	liver
47	chr4:101941800-101942600	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr4:101941800-101942600	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr4:101941800-101942800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr4:101941800-101942800	Enhancers	Primary B cells from peripheral blood	blood

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