Variant report

Variant	rs198584
Chromosome Location	chr13:49035467-49035468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11148110	0.83[EUR][1000 genomes]
rs12875750	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12877954	0.84[EUR][1000 genomes]
rs1359688	0.82[EUR][1000 genomes]
rs1536396	0.83[EUR][1000 genomes]
rs1536397	0.84[EUR][1000 genomes]
rs1573601	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs1894255	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs1951775	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs1981434	0.85[CEU][hapmap]
rs198563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs198570	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs198590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs198604	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]
rs198607	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs198612	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198619	0.85[CEU][hapmap]
rs2104532	0.85[EUR][1000 genomes]
rs2407095	0.83[EUR][1000 genomes]
rs2897588	0.81[EUR][1000 genomes]
rs3020645	0.85[EUR][1000 genomes]
rs3092904	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4151450	0.85[CEU][hapmap]
rs4635233	0.85[EUR][1000 genomes]
rs520342	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs7139578	0.90[CEU][hapmap];0.83[TSI][hapmap]
rs8002098	0.85[EUR][1000 genomes]
rs9316381	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]
rs9316382	0.86[EUR][1000 genomes]
rs9316388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs9316393	0.89[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs9316395	0.90[CEU][hapmap];0.83[TSI][hapmap]
rs9316399	0.90[CEU][hapmap]
rs9331991	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs943278	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs943283	0.81[EUR][1000 genomes]
rs9526481	0.84[EUR][1000 genomes]
rs9526483	0.83[EUR][1000 genomes]
rs9535006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs9535009	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs9535032	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs9535035	0.86[EUR][1000 genomes]
rs9535038	0.86[EUR][1000 genomes]
rs9535042	0.83[EUR][1000 genomes]
rs9535043	0.83[EUR][1000 genomes]
rs9535045	0.83[EUR][1000 genomes]
rs9535046	0.84[EUR][1000 genomes]
rs9562819	0.80[CEU][hapmap]
rs9568029	0.85[CEU][hapmap]
rs9568035	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9568043	0.85[EUR][1000 genomes]
rs9568047	0.91[EUR][1000 genomes]
rs9568049	0.84[EUR][1000 genomes]
rs9568050	0.84[EUR][1000 genomes]
rs9634680	0.85[EUR][1000 genomes]
rs990814	0.90[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs198584	LRCH1	cis	parietal	SCAN
rs198584	LOC220097	cis	multi-tissue	Pritchard
rs198584	LPAR6	cis	parietal	SCAN
rs198584	ATAD2	trans	parietal	SCAN
rs198584	ITM2B	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 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	chr13:49021200-49058600	Weak transcription	Hela-S3	cervix
5	chr13:49023800-49061000	Weak transcription	Small Intestine	intestine
6	chr13:49023800-49073800	Weak transcription	NH-A	brain
7	chr13:49024000-49059000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr13:49025600-49041200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr13:49025600-49056800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr13:49025600-49066200	Weak transcription	Psoas Muscle	Psoas
11	chr13:49026600-49039400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr13:49026800-49039400	Strong transcription	Dnd41	blood
13	chr13:49026800-49039600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr13:49027000-49039800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr13:49027200-49039200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:49027200-49039600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr13:49027200-49039800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr13:49027400-49036800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr13:49027400-49039800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:49027600-49039800	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr13:49027600-49049200	Weak transcription	A549	lung
22	chr13:49027800-49039200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr13:49027800-49043000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr13:49028000-49039200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr13:49028000-49071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr13:49028600-49039800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr13:49029000-49038600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr13:49029000-49038600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr13:49029000-49046000	Weak transcription	HSMMtube	muscle
30	chr13:49029200-49038800	Weak transcription	Osteobl	bone
31	chr13:49029200-49062000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr13:49029400-49052400	Weak transcription	K562	blood
33	chr13:49030000-49036400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr13:49030200-49037000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr13:49030400-49038200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr13:49030600-49070600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr13:49030800-49038800	Weak transcription	HUVEC	blood vessel
38	chr13:49031000-49039600	Strong transcription	Fetal Thymus	thymus
39	chr13:49031600-49038600	Weak transcription	GM12878-XiMat	blood
40	chr13:49031600-49049600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr13:49031600-49055800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr13:49031600-49066200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr13:49031800-49041200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr13:49031800-49045800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr13:49031800-49052000	Weak transcription	HepG2	liver
46	chr13:49031800-49052600	Weak transcription	Placenta	Placenta
47	chr13:49031800-49059200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr13:49031800-49060200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr13:49031800-49060600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr13:49031800-49065400	Weak transcription	Brain Substantia Nigra	brain

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