Variant report

Variant	rs907398
Chromosome Location	chr15:77772003-77772004
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	chr15:77767690..77769969-chr15:77771250..77773032,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11853696	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11858844	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12324211	0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12324795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12912084	0.81[ASN][1000 genomes]
rs13380202	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16968897	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs17384809	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17385059	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17385352	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17470529	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17470952	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17471252	0.83[ASN][1000 genomes]
rs17471431	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17471480	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17471697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17471753	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17472200	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2012740	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2012756	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2137111	0.82[JPT][hapmap]
rs2307141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28437977	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2864840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3784787	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3784788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4592615	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs4886863	0.81[ASN][1000 genomes]
rs4886864	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886865	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886874	0.82[JPT][hapmap]
rs56097641	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59204923	0.83[EUR][1000 genomes]
rs59362734	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59386622	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61306472	0.83[EUR][1000 genomes]
rs62007297	0.83[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs74026910	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74026912	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74026913	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74026918	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74026923	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74026925	0.94[EUR][1000 genomes]
rs74026926	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8035526	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs883627	0.94[JPT][hapmap]
rs907371	0.82[JPT][hapmap]

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
rs907398	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77750400-77777800	Strong transcription	Primary B cells from peripheral blood	blood
2	chr15:77750600-77777800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:77750600-77779200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:77750600-77779600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:77750800-77780400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:77751000-77773600	Weak transcription	Stomach Mucosa	stomach
7	chr15:77753400-77777600	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr15:77755200-77775600	Strong transcription	Duodenum Mucosa	Duodenum
9	chr15:77755400-77777800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr15:77756200-77778400	Strong transcription	Fetal Thymus	thymus
11	chr15:77756800-77775800	Weak transcription	Pancreas	Pancrea
12	chr15:77757200-77774200	Weak transcription	NHLF	lung
13	chr15:77759200-77776000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:77761600-77775800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:77762000-77775800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr15:77764600-77774800	Weak transcription	Fetal Brain Male	brain
17	chr15:77764600-77775400	Weak transcription	Brain Germinal Matrix	brain
18	chr15:77765200-77775400	Weak transcription	Right Ventricle	heart
19	chr15:77766000-77772400	Strong transcription	HSMM	muscle
20	chr15:77767200-77777400	Strong transcription	GM12878-XiMat	blood
21	chr15:77767600-77777600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:77767800-77772200	Strong transcription	NH-A	brain
23	chr15:77768000-77773400	Weak transcription	Brain Angular Gyrus	brain
24	chr15:77768000-77773600	Strong transcription	Hela-S3	cervix
25	chr15:77768600-77773800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:77769000-77773800	Strong transcription	Fetal Intestine Large	intestine
27	chr15:77769200-77773400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:77769400-77772600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:77769400-77772600	Strong transcription	HMEC	breast
30	chr15:77769400-77772800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:77769400-77773400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:77769400-77773600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:77769400-77773800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:77769400-77773800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr15:77769400-77774000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr15:77769400-77774600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:77769400-77777600	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr15:77769400-77777600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr15:77769400-77777800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:77769400-77777800	Strong transcription	HepG2	liver
41	chr15:77769400-77778000	Strong transcription	Dnd41	blood
42	chr15:77769400-77779800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:77769600-77772200	Strong transcription	Primary B cells from cord blood	blood
44	chr15:77769600-77772400	Strong transcription	K562	blood
45	chr15:77769600-77772600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:77769600-77773600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr15:77769600-77777600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:77769600-77777600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:77769600-77778000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr15:77769600-77778600	Strong transcription	Liver	Liver

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