Variant report

Variant	rs4994112
Chromosome Location	chr15:43014679-43014680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1058846	0.84[CEU][hapmap]
rs1206698	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs12102055	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12594483	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap]
rs12594855	0.89[CHB][hapmap]
rs12594951	0.87[ASW][hapmap]
rs12902830	0.84[CEU][hapmap]
rs12905385	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs12906497	0.90[CEU][hapmap];0.81[CHB][hapmap]
rs12917018	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap]
rs12917189	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs16957091	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap]
rs1705356	0.89[GIH][hapmap];0.85[MEX][hapmap]
rs17774047	0.84[CEU][hapmap]
rs1995939	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap]
rs2136899	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs2136900	0.89[CEU][hapmap]
rs2280048	0.84[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap]
rs2305084	0.90[CEU][hapmap]
rs2305085	1.00[CEU][hapmap]
rs2412741	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3099758	0.91[GIH][hapmap];0.85[MEX][hapmap]
rs3199486	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs3742987	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap]
rs3742988	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs3742993	0.81[TSI][hapmap]
rs4924690	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs4924694	0.89[CEU][hapmap];0.83[MEX][hapmap]
rs623271	0.89[GIH][hapmap]
rs6493060	1.00[ASW][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap]
rs6493061	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs6493067	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs6493068	1.00[ASW][hapmap];0.85[LWK][hapmap]
rs7163030	0.93[GIH][hapmap]
rs7166373	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs7166775	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs7167392	0.90[CEU][hapmap]
rs7167802	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs7169009	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap]
rs7169202	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7174041	0.94[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs7182141	0.80[CEU][hapmap]
rs7182753	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs731984	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs8023524	0.95[CEU][hapmap]
rs8026233	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap]
rs8027427	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap]
rs8030587	1.00[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs8031218	0.83[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs8034447	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs8035752	1.00[ASW][hapmap]
rs8036096	1.00[ASW][hapmap]
rs8039765	0.87[GIH][hapmap];0.84[MEX][hapmap]
rs8043472	1.00[ASW][hapmap];0.89[GIH][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap]
rs9269	0.89[CEU][hapmap]
rs9806175	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs9919994	0.84[CEU][hapmap];0.87[GIH][hapmap]
rs9920182	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv517553	chr15:42970899-43023482	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4994112	TGM5	cis	lymphoblastoid	seeQTL
rs4994112	BUB1B	cis	parietal	SCAN
rs4994112	MAP1A	cis	parietal	SCAN
rs4994112	CDAN1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
2	chr15:42976600-43015200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:42977000-43016600	Weak transcription	Hela-S3	cervix
4	chr15:42981400-43015000	Weak transcription	HSMM	muscle
5	chr15:42984000-43014800	Weak transcription	K562	blood
6	chr15:42986000-43018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:42987800-43016400	Weak transcription	Esophagus	oesophagus
8	chr15:42993400-43015400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:42997200-43016400	Weak transcription	Pancreas	Pancrea
10	chr15:43000800-43018600	Weak transcription	A549	lung
11	chr15:43001000-43014800	Weak transcription	HUVEC	blood vessel
12	chr15:43004200-43016200	Weak transcription	Psoas Muscle	Psoas
13	chr15:43007200-43026800	Strong transcription	Fetal Stomach	stomach
14	chr15:43007800-43020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:43008000-43027600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:43008200-43027600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:43008200-43027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:43008400-43020000	Strong transcription	Fetal Muscle Trunk	muscle
19	chr15:43008400-43020400	Strong transcription	Brain Substantia Nigra	brain
20	chr15:43008600-43027400	Strong transcription	Fetal Brain Female	brain
21	chr15:43008800-43017200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:43008800-43018400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr15:43008800-43019800	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr15:43008800-43026600	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:43008800-43027200	Strong transcription	Brain Germinal Matrix	brain
26	chr15:43008800-43027200	Strong transcription	Lung	lung
27	chr15:43008800-43027400	Strong transcription	Adipose Nuclei	Adipose
28	chr15:43008800-43027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:43009000-43027400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:43009000-43027600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr15:43009000-43027800	Strong transcription	Fetal Intestine Large	intestine
32	chr15:43009200-43014800	Weak transcription	Osteobl	bone
33	chr15:43009200-43027800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:43009400-43015200	Weak transcription	NHDF-Ad	bronchial
35	chr15:43009400-43015600	Weak transcription	Small Intestine	intestine
36	chr15:43009400-43017400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:43009400-43018200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr15:43009600-43026600	Strong transcription	Spleen	Spleen
39	chr15:43009600-43027400	Strong transcription	Fetal Intestine Small	intestine
40	chr15:43009600-43027800	Strong transcription	Left Ventricle	heart
41	chr15:43009800-43014800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:43009800-43016200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:43009800-43016200	Weak transcription	Fetal Brain Male	brain
44	chr15:43009800-43018600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:43009800-43020800	Weak transcription	Stomach Mucosa	stomach
46	chr15:43010000-43017200	Strong transcription	Colon Smooth Muscle	Colon
47	chr15:43010000-43020200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:43010000-43027200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:43010000-43027400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:43010000-43027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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