Variant report

Variant	rs2307141
Chromosome Location	chr15:77756418-77756419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11853696	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11856084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857330	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs11858844	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324016	0.83[ASN][1000 genomes]
rs12324211	0.87[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12324795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912084	0.84[ASN][1000 genomes]
rs13380202	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1493699	0.83[ASN][1000 genomes]
rs16968799	0.83[ASN][1000 genomes]
rs16968897	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs16968900	0.80[EUR][1000 genomes]
rs17384809	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17385059	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17385352	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17470529	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17470952	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471252	0.87[ASN][1000 genomes]
rs17471431	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471480	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17471753	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17472200	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2012740	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2012756	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2137111	0.82[JPT][hapmap]
rs2172587	0.83[ASN][1000 genomes]
rs28437977	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2864840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35651077	0.83[ASN][1000 genomes]
rs3784787	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3784788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4592615	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs4886863	0.84[ASN][1000 genomes]
rs4886864	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886865	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886874	0.82[JPT][hapmap]
rs56097641	0.87[EUR][1000 genomes]
rs59204923	0.83[EUR][1000 genomes]
rs59362734	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59386622	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61306472	0.83[EUR][1000 genomes]
rs62007297	0.86[ASN][1000 genomes]
rs62010566	0.83[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs74026910	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74026912	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74026913	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74026918	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74026923	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74026925	0.95[EUR][1000 genomes]
rs74026926	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8035526	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs883627	0.94[JPT][hapmap]
rs907371	0.82[JPT][hapmap]
rs907398	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]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2307141	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77730600-77758800	Weak transcription	Lung	lung
2	chr15:77743200-77763200	Weak transcription	Brain Germinal Matrix	brain
3	chr15:77748200-77766800	Weak transcription	Aorta	Aorta
4	chr15:77748400-77770600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:77749000-77757400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:77749000-77770400	Weak transcription	Spleen	Spleen
7	chr15:77749400-77757000	Weak transcription	Fetal Intestine Small	intestine
8	chr15:77749600-77763400	Weak transcription	Fetal Brain Male	brain
9	chr15:77749800-77758800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:77750000-77758000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:77750000-77758800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:77750000-77760600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr15:77750000-77763400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:77750000-77766400	Weak transcription	Psoas Muscle	Psoas
15	chr15:77750000-77770400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:77750200-77756600	Weak transcription	Pancreas	Pancrea
17	chr15:77750200-77757000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:77750200-77759000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:77750200-77759000	Weak transcription	Ovary	ovary
20	chr15:77750200-77763400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:77750200-77763800	Weak transcription	Right Ventricle	heart
22	chr15:77750200-77767000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:77750400-77759400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:77750400-77777800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr15:77750600-77758000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr15:77750600-77759000	Weak transcription	HMEC	breast
27	chr15:77750600-77759200	Weak transcription	Colon Smooth Muscle	Colon
28	chr15:77750600-77759400	Weak transcription	NHEK	skin
29	chr15:77750600-77777800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr15:77750600-77779200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:77750600-77779600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:77750800-77758800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:77750800-77758800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:77750800-77768200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:77750800-77768200	Strong transcription	Liver	Liver
36	chr15:77750800-77768200	Strong transcription	Fetal Intestine Large	intestine
37	chr15:77750800-77768400	Strong transcription	Primary T cells from cord blood	blood
38	chr15:77750800-77780400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:77751000-77757200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:77751000-77759000	Weak transcription	Small Intestine	intestine
41	chr15:77751000-77762600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:77751000-77766200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr15:77751000-77768600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:77751000-77770600	Weak transcription	Gastric	stomach
45	chr15:77751000-77770600	Weak transcription	Right Atrium	heart
46	chr15:77751000-77773600	Weak transcription	Stomach Mucosa	stomach
47	chr15:77751200-77756600	Weak transcription	NHLF	lung
48	chr15:77751200-77757800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr15:77751200-77759600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr15:77751800-77756600	Weak transcription	Muscle Satellite Cultured Cells	--

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