Variant report

Variant	rs198604
Chromosome Location	chr13:48984063-48984064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48979509..48982464-chr13:48983015..48985946,2	MCF-7	breast:
2	chr13:48979885..48981623-chr13:48983630..48986045,2	K562	blood:

Variant related genes	Relation type
ENSG00000139679	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12100135	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs12430215	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs12583516	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12871662	0.81[EUR][1000 genomes]
rs12875750	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs1573601	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs1894255	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925744	0.80[EUR][1000 genomes]
rs1925745	0.80[EUR][1000 genomes]
rs1981434	0.81[CEU][hapmap]
rs198561	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198563	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs198570	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs198584	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]
rs198590	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198607	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	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198619	0.81[CEU][hapmap]
rs198634	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2248488	0.81[CEU][hapmap]
rs2854345	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2854355	0.82[EUR][1000 genomes]
rs3020645	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3092904	0.90[AFR][1000 genomes]
rs375105	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803188	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs3809328	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs3818455	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs399413	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs4151450	0.81[CEU][hapmap]
rs4151520	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4151635	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs431406	0.85[EUR][1000 genomes]
rs471911	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942765	0.84[EUR][1000 genomes]
rs520342	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61973349	0.81[EUR][1000 genomes]
rs7984795	0.81[CEU][hapmap]
rs9316367	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs9316369	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs9316381	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]
rs9316388	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs9316393	0.93[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs9331991	0.94[CHB][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs9332032	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9526465	0.81[CEU][hapmap]
rs9526466	0.80[EUR][1000 genomes]
rs9526475	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs9534998	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs9535000	0.80[EUR][1000 genomes]
rs9535003	0.80[EUR][1000 genomes]
rs9535006	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs9535009	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs9562819	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9568027	0.81[EUR][1000 genomes]
rs9568028	0.81[EUR][1000 genomes]
rs9568029	0.81[CEU][hapmap]
rs9568032	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568033	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568034	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568035	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs198604	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs198604	ITM2B	cis	lymphoblastoid	seeQTL
rs198604	ATAD2	trans	parietal	SCAN

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	chr13:48966400-48986000	Weak transcription	Lung	lung
5	chr13:48966800-48984200	Weak transcription	Placenta	Placenta
6	chr13:48968800-48984200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr13:48969000-48984200	Weak transcription	Fetal Intestine Large	intestine
8	chr13:48969000-48984400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr13:48969200-48984200	Weak transcription	Fetal Stomach	stomach
10	chr13:48969200-48984400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr13:48970600-48984200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:48974600-48986000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr13:48975200-48984200	Weak transcription	Fetal Intestine Small	intestine
14	chr13:48975200-48985400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr13:48975400-48984200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr13:48975600-48985200	Weak transcription	NH-A	brain
17	chr13:48976000-48984200	Weak transcription	Primary B cells from cord blood	blood
18	chr13:48976000-48984200	Weak transcription	A549	lung
19	chr13:48976000-48984200	Weak transcription	NHLF	lung
20	chr13:48976000-48984400	Weak transcription	HSMMtube	muscle
21	chr13:48976000-49005800	Weak transcription	Hela-S3	cervix
22	chr13:48977600-48984200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr13:48977800-48984200	Weak transcription	Fetal Lung	lung
24	chr13:48977800-48984200	Weak transcription	NHDF-Ad	bronchial
25	chr13:48977800-48984400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr13:48977800-48984400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr13:48978000-48984200	Weak transcription	Osteobl	bone
28	chr13:48978400-48984200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:48978400-48984400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr13:48978400-48985200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr13:48978400-48985400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr13:48978400-48986000	Weak transcription	Esophagus	oesophagus
33	chr13:48978400-48989800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr13:48978800-48990400	Weak transcription	Spleen	Spleen
35	chr13:48979000-48984200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr13:48979600-48984200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:48980200-48984200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr13:48981000-48984200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr13:48981200-48985400	Weak transcription	HSMM	muscle
40	chr13:48981200-48987600	Active TSS	Right Atrium	heart
41	chr13:48982200-48987600	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr13:48982400-48987200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr13:48982600-48984200	Active TSS	Adipose Nuclei	Adipose
44	chr13:48982600-48984600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr13:48983000-48984200	Active TSS	Primary monocytes fromperipheralblood	blood
46	chr13:48983000-48984400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr13:48983000-48984400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr13:48983000-48985600	Active TSS	HepG2	liver
49	chr13:48983000-48987400	Active TSS	Brain Anterior Caudate	brain
50	chr13:48983000-48987600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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