Variant report

Variant	rs11630497
Chromosome Location	chr15:77334787-77334788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:77334610-77335231	HL-60	blood:	n/a	n/a
2	POLR2A	chr15:77333901-77336487	HL-60	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:77332598..77335104-chr15:77338074..77339723,2	MCF-7	breast:
2	chr15:77327656..77329511-chr15:77332033..77335172,3	K562	blood:
3	chr15:77333192..77335092-chr15:77340971..77343309,2	MCF-7	breast:
4	chr15:77334649..77338471-chr15:77361377..77364899,5	K562	blood:
5	chr15:77327656..77330194-chr15:77332164..77335172,3	K562	blood:
6	chr15:77334559..77338244-chr15:77361377..77364599,4	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSPAN3-1	chr15:77334178-77335533	ENSG00000260787.1
2	lnc-TSPAN3-1	chr15:77334178-77335144	NONHSAT047418

No data

Variant related genes	Relation type
ENSG00000259652	TF binding region
ENSG00000140391	Chromatin interaction
ENSG00000140368	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11072641	0.85[AMR][1000 genomes]
rs11636613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636648	1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11737	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12148761	0.96[CEU][hapmap]
rs12372961	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[ASN][1000 genomes]
rs12901188	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12912792	0.80[ASN][1000 genomes]
rs16968665	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.84[ASN][1000 genomes]
rs2404233	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs2404234	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs34443712	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3935339	0.86[JPT][hapmap]
rs4078354	0.87[CEU][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap]
rs4886509	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886847	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs55645420	0.80[ASN][1000 genomes]
rs7166154	0.96[CEU][hapmap]
rs7169831	1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7177533	0.81[CHB][hapmap]
rs8032	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9806416	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1048833	chr15:77294593-77339260	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904414	chr15:77304310-77400388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv570117	chr15:77327571-77334787	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv511547	chr15:77328269-77337649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11630497	TSPAN3	cis	cerebellum	SCAN
rs11630497	RP11-797A18.4	cis	Muscle Skeletal	GTEx
rs11630497	RP11-797A18.4	cis	Esophagus Muscularis	GTEx
rs11630497	ISL2	cis	cerebellum	SCAN
rs11630497	RP11-797A18.4	cis	lung	GTEx
rs11630497	PSTPIP1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77318400-77350600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:77321200-77335400	Weak transcription	Left Ventricle	heart
3	chr15:77321200-77362000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:77323000-77336000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:77323400-77346000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:77324200-77335200	Weak transcription	NH-A	brain
7	chr15:77326400-77335200	Weak transcription	HepG2	liver
8	chr15:77326800-77334800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:77326800-77349800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:77327400-77336400	Weak transcription	Psoas Muscle	Psoas
11	chr15:77327400-77346000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:77327600-77335200	Weak transcription	Ovary	ovary
13	chr15:77327600-77335800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr15:77327600-77338000	Weak transcription	NHDF-Ad	bronchial
15	chr15:77327800-77335200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:77327800-77346800	Strong transcription	Primary B cells from cord blood	blood
17	chr15:77328000-77338600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:77328000-77344400	Weak transcription	Small Intestine	intestine
19	chr15:77328200-77335400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr15:77328400-77336000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr15:77328600-77336000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:77328600-77336400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr15:77328600-77337400	Weak transcription	Brain Substantia Nigra	brain
24	chr15:77329200-77335200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:77329600-77336600	Weak transcription	Esophagus	oesophagus
26	chr15:77329600-77339600	Strong transcription	Primary hematopoietic stem cells	blood
27	chr15:77329800-77336000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:77330000-77335400	Weak transcription	Dnd41	blood
29	chr15:77330000-77335800	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:77330000-77337000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:77330000-77338800	Weak transcription	Aorta	Aorta
32	chr15:77330000-77352000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr15:77330000-77352200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr15:77330200-77335200	Weak transcription	Colonic Mucosa	Colon
35	chr15:77330200-77336000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:77330200-77336200	Weak transcription	NHLF	lung
37	chr15:77330200-77337000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:77330200-77352400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:77330400-77334800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:77330400-77334800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:77330400-77335000	Weak transcription	Spleen	Spleen
42	chr15:77330400-77335200	Weak transcription	Pancreas	Pancrea
43	chr15:77330400-77335200	Weak transcription	Right Ventricle	heart
44	chr15:77330400-77335200	Weak transcription	HSMMtube	muscle
45	chr15:77330400-77335400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:77330400-77335800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr15:77330400-77336000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr15:77330400-77336400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:77330400-77336800	Weak transcription	GM12878-XiMat	blood
50	chr15:77330400-77338000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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