Variant report

Variant	rs1374201
Chromosome Location	chr15:77477873-77477874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77477542..77479471-chr15:77711418..77713523,2	MCF-7	breast:
2	chr15:77461714..77464507-chr15:77477609..77479854,2	K562	blood:

Variant related genes	Relation type
ENSG00000173517	Chromatin interaction
ENSG00000140382	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1015813	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10519158	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11853625	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11853633	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11854182	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11854466	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11856513	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11856538	0.93[CHD][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.88[ASN][1000 genomes]
rs11857330	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs11857804	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12148274	0.82[ASN][1000 genomes]
rs12324366	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12900110	0.89[ASN][1000 genomes]
rs12902106	0.86[ASN][1000 genomes]
rs12902434	0.86[ASN][1000 genomes]
rs12902446	0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12912963	0.82[ASN][1000 genomes]
rs13379686	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13380152	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1446313	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16968730	0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs17381652	0.84[CHB][hapmap];0.87[ASN][1000 genomes]
rs17381821	0.84[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17383078	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17385296	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs17466480	0.90[ASN][1000 genomes]
rs17468413	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1867780	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2044453	0.93[CHB][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs2137977	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292594	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.97[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2864079	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34572155	0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs35093280	0.87[ASN][1000 genomes]
rs4592615	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4638539	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886514	0.86[ASN][1000 genomes]
rs4886852	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886857	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55881066	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55994208	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56070388	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58792939	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59831220	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60079927	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60761381	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60863150	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7173670	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7182221	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74025074	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74025104	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74025105	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74027548	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74027549	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7496431	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[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	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	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
3	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
4	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
5	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1374201	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77451000-77478800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr15:77451200-77491800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:77460800-77479200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr15:77461600-77496800	Weak transcription	Lung	lung
5	chr15:77465400-77488200	Weak transcription	Psoas Muscle	Psoas
6	chr15:77466200-77479000	Weak transcription	Brain Anterior Caudate	brain
7	chr15:77466200-77479400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:77467200-77491400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:77469000-77480200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:77469400-77483800	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:77469800-77491200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:77469800-77499200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:77471000-77479000	Weak transcription	Brain Angular Gyrus	brain
14	chr15:77471000-77482600	Weak transcription	Fetal Brain Male	brain
15	chr15:77471400-77505800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:77471600-77479200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:77471600-77481600	Weak transcription	Pancreas	Pancrea
18	chr15:77471800-77481400	Weak transcription	Spleen	Spleen
19	chr15:77471800-77482000	Weak transcription	Colonic Mucosa	Colon
20	chr15:77471800-77491400	Weak transcription	Aorta	Aorta
21	chr15:77472000-77479200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:77472000-77479200	Weak transcription	NHLF	lung
23	chr15:77472200-77479200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:77472200-77479400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:77472200-77480000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:77472400-77500800	Weak transcription	HSMMtube	muscle
27	chr15:77472800-77479600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:77472800-77480000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:77473000-77478600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:77473000-77483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:77473200-77478400	Weak transcription	Fetal Intestine Large	intestine
32	chr15:77473400-77479200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:77473400-77479200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:77473600-77479000	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:77473600-77479000	Weak transcription	Small Intestine	intestine
36	chr15:77473600-77479800	Weak transcription	Right Atrium	heart
37	chr15:77473600-77527800	Weak transcription	Placenta	Placenta
38	chr15:77473800-77478800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:77474000-77480000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:77474000-77480000	Weak transcription	HSMM	muscle
41	chr15:77474200-77478800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr15:77474200-77479000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:77474200-77479000	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:77474200-77479200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:77474200-77479200	Weak transcription	Fetal Stomach	stomach
46	chr15:77474200-77479200	Weak transcription	NH-A	brain
47	chr15:77474200-77479200	Weak transcription	Osteobl	bone
48	chr15:77474200-77480000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:77474200-77482400	Enhancers	Primary B cells from peripheral blood	blood
50	chr15:77474200-77490600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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