Variant report

Variant	rs17472200
Chromosome Location	chr15:77783812-77783813
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77745907..77748744-chr15:77783742..77785823,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11853696	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11856084	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858844	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12324211	0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12324632	0.87[YRI][hapmap]
rs12324795	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13380202	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16968897	0.91[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16968900	0.80[EUR][1000 genomes]
rs17384809	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17385059	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17385352	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17470529	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17470952	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17471431	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471480	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471697	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17471753	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2012740	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2012756	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2137111	0.82[JPT][hapmap]
rs2307141	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28437977	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2864840	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3784787	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3784788	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886864	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886865	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886874	0.82[JPT][hapmap]
rs56097641	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59204923	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs59362734	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59386622	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61306472	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7182221	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs74026910	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74026912	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74026913	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74026918	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74026923	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74026925	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74026926	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8035526	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs883627	0.94[JPT][hapmap]
rs907371	0.82[JPT][hapmap]
rs907398	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17472200	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77770000-77789200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:77776200-77787600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:77776200-77788200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:77776200-77789000	Weak transcription	Colonic Mucosa	Colon
5	chr15:77776400-77788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:77776800-77785600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:77776800-77788200	Weak transcription	Lung	lung
8	chr15:77777000-77788000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:77777400-77785200	Weak transcription	GM12878-XiMat	blood
10	chr15:77777400-77785400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:77777400-77786400	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:77777400-77787800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr15:77777400-77788000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:77777400-77788000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:77777400-77788800	Weak transcription	Hela-S3	cervix
16	chr15:77777600-77785400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:77777600-77785600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:77777600-77785600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:77777600-77785600	Weak transcription	Thymus	Thymus
20	chr15:77777600-77787400	Weak transcription	Fetal Brain Female	brain
21	chr15:77777600-77787600	Weak transcription	Fetal Brain Male	brain
22	chr15:77777600-77787800	Weak transcription	Pancreas	Pancrea
23	chr15:77777600-77788200	Weak transcription	Brain Germinal Matrix	brain
24	chr15:77777600-77789000	Weak transcription	Fetal Intestine Large	intestine
25	chr15:77777600-77789400	Weak transcription	Aorta	Aorta
26	chr15:77777600-77789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:77777600-77798600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:77777800-77785200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr15:77777800-77785200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:77777800-77785400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:77777800-77785400	Weak transcription	NH-A	brain
32	chr15:77777800-77785600	Weak transcription	Placenta	Placenta
33	chr15:77777800-77788000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:77777800-77788000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:77777800-77788600	Weak transcription	HepG2	liver
36	chr15:77777800-77789000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:77777800-77789000	Weak transcription	A549	lung
38	chr15:77778000-77785400	Weak transcription	Osteobl	bone
39	chr15:77778000-77785600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr15:77778000-77788000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:77778200-77785400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:77778200-77787400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr15:77778200-77788200	Weak transcription	Esophagus	oesophagus
44	chr15:77778600-77785200	Weak transcription	Liver	Liver
45	chr15:77779000-77785400	Weak transcription	Fetal Thymus	thymus
46	chr15:77779200-77788600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:77779400-77785400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr15:77779400-77788400	Weak transcription	HMEC	breast
49	chr15:77779600-77784800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:77779600-77784800	Weak transcription	Brain Angular Gyrus	brain

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