Variant report

Variant	rs9316381
Chromosome Location	chr13:49068419-49068420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49063272..49066257-chr13:49067561..49069081,2	K562	blood:
2	chr13:49064757..49067579-chr13:49067581..49069606,2	K562	blood:

Variant related genes	Relation type
ENSG00000136161	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11148110	0.83[EUR][1000 genomes]
rs12583516	0.85[AFR][1000 genomes]
rs12855185	0.80[EUR][1000 genomes]
rs12876717	0.80[EUR][1000 genomes]
rs12877288	0.80[EUR][1000 genomes]
rs12877954	0.85[EUR][1000 genomes]
rs1359688	0.83[EUR][1000 genomes]
rs1536396	0.83[EUR][1000 genomes]
rs1536397	0.85[EUR][1000 genomes]
rs1573601	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap]
rs1894255	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs1951775	0.90[CEU][hapmap]
rs1981434	0.85[CEU][hapmap]
rs198561	0.82[AFR][1000 genomes]
rs198563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs198570	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs198584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs198590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198604	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs198607	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs198612	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198619	0.85[CEU][hapmap]
rs2104532	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2407095	0.84[EUR][1000 genomes]
rs2897588	0.81[EUR][1000 genomes]
rs3020645	0.85[EUR][1000 genomes]
rs3092904	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs375105	0.82[AFR][1000 genomes]
rs4151450	0.85[CEU][hapmap]
rs431406	0.80[AFR][1000 genomes]
rs4635233	0.85[EUR][1000 genomes]
rs471911	0.85[AFR][1000 genomes]
rs520342	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs7139578	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs8002098	0.84[EUR][1000 genomes]
rs9316382	0.85[EUR][1000 genomes]
rs9316388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9316393	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9316395	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs9316399	0.90[CEU][hapmap]
rs9316407	0.80[EUR][1000 genomes]
rs9331991	0.94[CHB][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs943278	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs943283	0.81[EUR][1000 genomes]
rs9526481	0.85[EUR][1000 genomes]
rs9526483	0.83[EUR][1000 genomes]
rs9535032	0.90[CEU][hapmap]
rs9535035	0.85[EUR][1000 genomes]
rs9535038	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9535042	0.84[EUR][1000 genomes]
rs9535043	0.83[EUR][1000 genomes]
rs9535045	0.84[EUR][1000 genomes]
rs9535046	0.85[EUR][1000 genomes]
rs9535049	0.80[EUR][1000 genomes]
rs9562819	0.80[CEU][hapmap]
rs9568029	0.85[CEU][hapmap]
rs9568032	0.89[AFR][1000 genomes]
rs9568033	0.86[AFR][1000 genomes]
rs9568034	0.89[AFR][1000 genomes]
rs9568035	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9568043	0.84[EUR][1000 genomes]
rs9568047	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9568049	0.85[EUR][1000 genomes]
rs9568050	0.85[EUR][1000 genomes]
rs9634680	0.85[EUR][1000 genomes]
rs990814	0.90[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' 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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9316381	LPAR6	cis	parietal	SCAN
rs9316381	ATAD2	trans	parietal	SCAN
rs9316381	ITM2B	cis	lymphoblastoid	seeQTL
rs9316381	LRCH1	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49023800-49073800	Weak transcription	NH-A	brain
2	chr13:49028000-49071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr13:49030600-49070600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr13:49034400-49073800	Weak transcription	Esophagus	oesophagus
5	chr13:49035200-49073400	Weak transcription	Fetal Intestine Small	intestine
6	chr13:49053600-49071200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:49061400-49072000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:49062600-49070800	Weak transcription	Fetal Brain Male	brain
10	chr13:49062800-49070400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr13:49062800-49072000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr13:49063000-49087800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr13:49063200-49071000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:49064200-49069800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:49064200-49075200	Weak transcription	Fetal Intestine Large	intestine
16	chr13:49064400-49068800	Flanking Active TSS	Dnd41	blood
17	chr13:49064600-49070600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr13:49064800-49071200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr13:49065000-49069800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr13:49065000-49070200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr13:49065400-49069400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr13:49065400-49072000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr13:49065600-49069000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr13:49066600-49069000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr13:49066800-49073200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr13:49066800-49080200	Weak transcription	Colonic Mucosa	Colon
27	chr13:49067000-49068600	Enhancers	HUVEC	blood vessel
28	chr13:49067000-49068800	Enhancers	Liver	Liver
29	chr13:49067000-49068800	Enhancers	Fetal Thymus	thymus
30	chr13:49067000-49069000	Enhancers	HMEC	breast
31	chr13:49067000-49069000	Enhancers	HSMM	muscle
32	chr13:49067000-49069400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:49067000-49070200	Weak transcription	Aorta	Aorta
34	chr13:49067000-49071400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr13:49067000-49071600	Weak transcription	HepG2	liver
36	chr13:49067000-49072800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr13:49067000-49074600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr13:49067000-49080200	Weak transcription	Psoas Muscle	Psoas
39	chr13:49067000-49084200	Weak transcription	Ovary	ovary
40	chr13:49067200-49068600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr13:49067200-49068600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr13:49067200-49068600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr13:49067200-49068600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr13:49067200-49068800	Enhancers	Primary T cells from cord blood	blood
45	chr13:49067200-49069000	Enhancers	Primary T cells fromperipheralblood	blood
46	chr13:49067200-49069000	Enhancers	Primary hematopoietic stem cells	blood
47	chr13:49067200-49069000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr13:49067200-49069000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr13:49067200-49069000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr13:49067200-49069000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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