Variant report

Variant	rs13064311
Chromosome Location	chr3:42638261-42638262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:42636237-42639709	K562	blood:	n/a	n/a
2	POLR2A	chr3:42637857-42638889	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:42636950-42639278	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:42638180-42638380	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
2	chr3:42631664..42634178-chr3:42636385..42639345,6	MCF-7	breast:
3	chr3:42603400..42605797-chr3:42635471..42638332,2	MCF-7	breast:
4	chr13:31036112..31036612-chr3:42637972..42638473,2	NB4	blood:
5	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SS18L2-1	chr3:42638189-42638523	expReg_chr3_3295_+

No data

Variant related genes	Relation type
NKTR	TF binding region
ENSG00000093183	Chromatin interaction
ENSG00000114853	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000230084	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs13066173	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13066333	0.86[ASN][1000 genomes]
rs168138	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2068278	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271181	0.86[ASN][1000 genomes]
rs2271184	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284305	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237064	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2940407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3095258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339656	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs339720	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs339721	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs339724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs339729	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs339735	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs342523	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342524	0.81[ASN][1000 genomes]
rs342526	0.82[ASN][1000 genomes]
rs342534	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs342535	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342538	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs383937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3888651	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs398743	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs60994254	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs637852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs638904	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs651180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs654761	0.93[ASN][1000 genomes]
rs663258	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs664813	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs665206	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs704982	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs807863	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs82755	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs9311323	0.92[ASN][1000 genomes]
rs9311324	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9813479	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819563	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9828279	0.86[EUR][1000 genomes];0.99[ASN][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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13064311	NKTR	cis	parietal	SCAN
rs13064311	NKTR	cis	cerebellum	SCAN
rs13064311	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42633200-42641400	Weak transcription	Aorta	Aorta
2	chr3:42633200-42641600	Weak transcription	Gastric	stomach
3	chr3:42633400-42641200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:42633400-42641200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:42633400-42641200	Weak transcription	HSMMtube	muscle
6	chr3:42633400-42641400	Weak transcription	Ovary	ovary
7	chr3:42633400-42641400	Weak transcription	Psoas Muscle	Psoas
8	chr3:42633400-42641400	Weak transcription	Right Ventricle	heart
9	chr3:42633400-42641600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:42633400-42641600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:42633400-42641600	Weak transcription	Esophagus	oesophagus
12	chr3:42633400-42641600	Weak transcription	Spleen	Spleen
13	chr3:42633600-42639200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:42633600-42639400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:42633600-42641200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:42633600-42641200	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:42633600-42641200	Weak transcription	Fetal Kidney	kidney
18	chr3:42633600-42641200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:42633600-42641200	Weak transcription	Right Atrium	heart
20	chr3:42633600-42641200	Weak transcription	NHEK	skin
21	chr3:42633600-42641400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:42633600-42641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:42633600-42641400	Weak transcription	Brain Anterior Caudate	brain
24	chr3:42633600-42641600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:42633600-42641600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:42633600-42641600	Weak transcription	Pancreas	Pancrea
27	chr3:42633800-42638600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:42633800-42638800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:42633800-42641200	Weak transcription	Brain Germinal Matrix	brain
30	chr3:42634000-42641200	Weak transcription	Fetal Intestine Small	intestine
31	chr3:42634000-42641600	Weak transcription	Lung	lung
32	chr3:42634200-42638800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:42634400-42641200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:42634600-42641200	Weak transcription	Fetal Brain Male	brain
35	chr3:42635000-42638600	Strong transcription	Primary B cells from cord blood	blood
36	chr3:42635000-42638600	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:42635000-42639400	Strong transcription	HSMM	muscle
38	chr3:42635000-42639600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:42635200-42638600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:42635200-42638800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:42635400-42638600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:42635400-42638600	Strong transcription	HMEC	breast
43	chr3:42635400-42641200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:42635400-42641200	Weak transcription	Brain Angular Gyrus	brain
45	chr3:42635600-42638600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr3:42635600-42638600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:42635600-42638800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:42635600-42640800	Weak transcription	Hela-S3	cervix
49	chr3:42635600-42641200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:42635600-42641200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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