Variant report

Variant	rs198607
Chromosome Location	chr13:48979167-48979168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11839271	0.82[EUR][1000 genomes]
rs12100135	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs12583516	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12875750	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1573601	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap]
rs1894255	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1951775	0.81[CEU][hapmap]
rs1981434	0.85[CEU][hapmap]
rs198561	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198563	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs198570	0.82[ASN][1000 genomes]
rs198584	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs198590	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198604	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198612	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198619	0.85[CEU][hapmap]
rs198634	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2243626	0.81[CEU][hapmap]
rs2248488	0.85[CEU][hapmap]
rs2854345	0.80[ASN][1000 genomes]
rs3020645	0.83[ASN][1000 genomes]
rs3092904	0.86[AFR][1000 genomes]
rs375105	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803188	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs3809328	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs3818455	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap]
rs4151450	0.85[CEU][hapmap]
rs4151520	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4151635	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs431406	0.84[EUR][1000 genomes]
rs471911	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520342	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7139578	0.81[CEU][hapmap]
rs7984795	0.85[CEU][hapmap]
rs9316367	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap]
rs9316369	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9316381	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs9316388	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs9316393	0.93[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap]
rs9316395	0.81[CEU][hapmap]
rs9316399	0.81[CEU][hapmap]
rs9331991	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs9332032	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs943278	0.81[CEU][hapmap]
rs9526465	0.85[CEU][hapmap]
rs9534998	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]
rs9535006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap]
rs9535009	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap]
rs9535032	0.81[CEU][hapmap]
rs9568029	0.85[CEU][hapmap]
rs9568032	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9568033	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9568034	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9568035	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs990814	0.81[CEU][hapmap]

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	esv1803998	chr13:48966078-48986320	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1050786	chr13:48971510-48987032	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1053432	chr13:48971510-48992810	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1043486	chr13:48971510-48996995	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs198607	ATAD2	trans	parietal	SCAN
rs198607	LRCH1	cis	parietal	SCAN
rs198607	MED4	cis	cerebellum	SCAN
rs198607	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs198607	ITM2B	cis	lymphoblastoid	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48916800-48985400	Weak transcription	Colonic Mucosa	Colon
2	chr13:48934600-48984200	Weak transcription	Right Ventricle	heart
3	chr13:48943600-48984200	Weak transcription	Brain Angular Gyrus	brain
4	chr13:48944600-48983400	Weak transcription	Psoas Muscle	Psoas
5	chr13:48966400-48986000	Weak transcription	Lung	lung
6	chr13:48966800-48984200	Weak transcription	Placenta	Placenta
7	chr13:48968800-48984200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr13:48969000-48984200	Weak transcription	Fetal Intestine Large	intestine
9	chr13:48969000-48984400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr13:48969200-48984200	Weak transcription	Fetal Stomach	stomach
11	chr13:48969200-48984400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr13:48970600-48984200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:48972000-48980000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:48972600-48982600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr13:48973800-48984000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr13:48974600-48986000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:48975200-48979800	Weak transcription	Fetal Heart	heart
18	chr13:48975200-48980600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr13:48975200-48983800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr13:48975200-48984000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr13:48975200-48984200	Weak transcription	Fetal Intestine Small	intestine
22	chr13:48975200-48985400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr13:48975400-48983000	Weak transcription	Brain Hippocampus Middle	brain
24	chr13:48975400-48984200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr13:48975600-48980800	Weak transcription	HSMM	muscle
26	chr13:48975600-48983000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr13:48975600-48984000	Weak transcription	Stomach Mucosa	stomach
28	chr13:48975600-48985200	Weak transcription	NH-A	brain
29	chr13:48975800-48980200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr13:48975800-48983000	Weak transcription	Fetal Kidney	kidney
31	chr13:48975800-48984000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr13:48976000-48984200	Weak transcription	Primary B cells from cord blood	blood
33	chr13:48976000-48984200	Weak transcription	A549	lung
34	chr13:48976000-48984200	Weak transcription	NHLF	lung
35	chr13:48976000-48984400	Weak transcription	HSMMtube	muscle
36	chr13:48976000-49005800	Weak transcription	Hela-S3	cervix
37	chr13:48976400-48979200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr13:48976800-48982000	Weak transcription	HepG2	liver
39	chr13:48976800-48983800	Weak transcription	Ovary	ovary
40	chr13:48977000-48984000	Weak transcription	Liver	Liver
41	chr13:48977000-48984000	Weak transcription	HUVEC	blood vessel
42	chr13:48977400-48979800	Active TSS	Right Atrium	heart
43	chr13:48977600-48980600	Weak transcription	Left Ventricle	heart
44	chr13:48977600-48983000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr13:48977600-48984000	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr13:48977600-48984200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr13:48977800-48979200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr13:48977800-48979200	Weak transcription	NHEK	skin
49	chr13:48977800-48979600	Weak transcription	Small Intestine	intestine
50	chr13:48977800-48980000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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