Variant report

Variant	rs990814
Chromosome Location	chr13:49059577-49059578
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49057919..49060518-chr13:49066120..49068824,2	K562	blood:
2	chr13:49058648..49060193-chr13:49061101..49062675,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136161	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12430215	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1573601	0.86[CEU][hapmap]
rs1894255	0.81[CEU][hapmap]
rs1951775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1981434	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs198563	0.90[CEU][hapmap]
rs198584	0.90[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs198590	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs198607	0.81[CEU][hapmap]
rs198612	0.86[CEU][hapmap]
rs198619	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2406935	0.88[EUR][1000 genomes]
rs2407093	0.83[EUR][1000 genomes]
rs2897588	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3092904	0.85[EUR][1000 genomes]
rs399413	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap]
rs4151450	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs4942765	0.85[AFR][1000 genomes]
rs520342	0.86[CEU][hapmap]
rs7139578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7329065	0.85[EUR][1000 genomes]
rs7333360	0.87[EUR][1000 genomes]
rs7336379	0.82[EUR][1000 genomes]
rs9316381	0.90[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs9316382	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316388	0.90[CEU][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs9316393	0.80[EUR][1000 genomes]
rs9316394	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9316395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs9316399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs943278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943283	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9526475	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9526479	0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs9535009	0.86[CEU][hapmap]
rs9535018	0.81[EUR][1000 genomes]
rs9535032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535033	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535035	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9562819	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9568029	0.95[CEU][hapmap]
rs9568042	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568043	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription 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	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs990814	LPAR6	cis	parietal	SCAN
rs990814	LOC100129597	cis	Lymphoblastoid	GTEx
rs990814	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs990814	ITM2B	cis	lymphoblastoid	seeQTL
rs990814	ATAD2	trans	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49017400-49062200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:49018000-49062400	Weak transcription	Fetal Brain Male	brain
3	chr13:49020800-49062000	Weak transcription	Fetal Kidney	kidney
4	chr13:49023800-49061000	Weak transcription	Small Intestine	intestine
5	chr13:49023800-49073800	Weak transcription	NH-A	brain
6	chr13:49025600-49066200	Weak transcription	Psoas Muscle	Psoas
7	chr13:49028000-49071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr13:49029200-49062000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:49030600-49070600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr13:49031600-49066200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr13:49031800-49060200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr13:49031800-49060600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr13:49031800-49065400	Weak transcription	Brain Substantia Nigra	brain
14	chr13:49032000-49065600	Weak transcription	Brain Anterior Caudate	brain
15	chr13:49032000-49066200	Weak transcription	Colonic Mucosa	Colon
16	chr13:49032400-49062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr13:49032400-49066200	Weak transcription	Spleen	Spleen
18	chr13:49032400-49066600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr13:49032400-49066600	Weak transcription	Ovary	ovary
20	chr13:49032400-49067400	Weak transcription	Pancreas	Pancrea
21	chr13:49032400-49067600	Weak transcription	Gastric	stomach
22	chr13:49032800-49066200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr13:49034400-49073800	Weak transcription	Esophagus	oesophagus
24	chr13:49035200-49073400	Weak transcription	Fetal Intestine Small	intestine
25	chr13:49035600-49065400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr13:49035600-49066000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr13:49035800-49061800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr13:49035800-49066400	Weak transcription	NHEK	skin
29	chr13:49039800-49062000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr13:49049600-49062200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr13:49049800-49060000	Strong transcription	Primary B cells from cord blood	blood
32	chr13:49049800-49066200	Weak transcription	Lung	lung
33	chr13:49050000-49061800	Weak transcription	Fetal Brain Female	brain
34	chr13:49050000-49065600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr13:49051200-49063600	Weak transcription	Primary T cells from cord blood	blood
36	chr13:49051200-49064800	Weak transcription	Brain Hippocampus Middle	brain
37	chr13:49051800-49065400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr13:49052000-49062000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr13:49052800-49063600	Weak transcription	Adipose Nuclei	Adipose
40	chr13:49052800-49064800	Weak transcription	Liver	Liver
41	chr13:49053000-49060400	Weak transcription	HepG2	liver
42	chr13:49053200-49063800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr13:49053600-49061000	Weak transcription	Fetal Stomach	stomach
44	chr13:49053600-49063200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr13:49053600-49071200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr13:49053800-49066600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr13:49054200-49060400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr13:49054200-49061400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr13:49054200-49062400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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