Variant report

Variant	rs17709377
Chromosome Location	chr15:42756619-42756620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10518763	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10518766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1060291	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1060293	1.00[ASN][1000 genomes]
rs10851410	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11022	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11070376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11636577	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12324717	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1659215	0.82[CEU][hapmap]
rs16973053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973054	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973059	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973089	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973091	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973093	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973095	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973096	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973097	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973107	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973109	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973132	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs16973137	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs16973148	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973153	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973155	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs16973171	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973174	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973175	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973320	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17695121	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs17709180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17766532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2412704	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2412709	0.82[CEU][hapmap]
rs28364347	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2899051	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2899059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34359922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34643746	1.00[ASN][1000 genomes]
rs34792942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3986280	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4344713	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4923948	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4924683	0.82[EUR][1000 genomes]
rs4924684	1.00[ASN][1000 genomes]
rs4924687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56357092	1.00[ASN][1000 genomes]
rs56982416	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58042601	1.00[ASN][1000 genomes]
rs58641431	1.00[ASN][1000 genomes]
rs59697584	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59705032	1.00[ASN][1000 genomes]
rs60380503	1.00[ASN][1000 genomes]
rs60584955	1.00[ASN][1000 genomes]
rs60812675	1.00[ASN][1000 genomes]
rs61489160	1.00[ASN][1000 genomes]
rs61753567	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62022317	1.00[ASN][1000 genomes]
rs7164437	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7164874	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7165023	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7178901	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7180483	1.00[ASN][1000 genomes]
rs7182797	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73402783	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73402785	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404714	1.00[ASN][1000 genomes]
rs73404717	0.82[EUR][1000 genomes]
rs73404723	1.00[ASN][1000 genomes]
rs73404730	1.00[ASN][1000 genomes]
rs73404763	1.00[ASN][1000 genomes]
rs73406518	1.00[ASN][1000 genomes]
rs73406534	1.00[ASN][1000 genomes]
rs73406545	1.00[ASN][1000 genomes]
rs74009095	1.00[ASN][1000 genomes]
rs8033412	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8037100	0.85[CEU][hapmap]
rs8038153	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17709377	LRRC57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42701200-42766600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:42720400-42759200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:42737200-42764800	Weak transcription	A549	lung
4	chr15:42744000-42757400	Weak transcription	Gastric	stomach
5	chr15:42744000-42757600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:42744200-42756800	Weak transcription	Dnd41	blood
7	chr15:42744200-42757000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:42744200-42757400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:42744200-42757400	Weak transcription	HepG2	liver
10	chr15:42744200-42757600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:42744200-42762200	Weak transcription	K562	blood
12	chr15:42744200-42763200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:42744200-42767000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:42744200-42781800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr15:42744200-42782400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:42749200-42761800	Weak transcription	Brain Germinal Matrix	brain
17	chr15:42749600-42764600	Weak transcription	Colonic Mucosa	Colon
18	chr15:42749800-42757400	Weak transcription	Placenta	Placenta
19	chr15:42749800-42758000	Weak transcription	Pancreas	Pancrea
20	chr15:42750000-42782600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:42750200-42763600	Weak transcription	Right Atrium	heart
22	chr15:42750200-42766400	Weak transcription	Right Ventricle	heart
23	chr15:42750200-42782400	Weak transcription	Aorta	Aorta
24	chr15:42750400-42756800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:42750400-42757200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:42750400-42757200	Weak transcription	Fetal Brain Female	brain
27	chr15:42750400-42761600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr15:42750400-42762800	Weak transcription	HMEC	breast
29	chr15:42750400-42765000	Weak transcription	Fetal Brain Male	brain
30	chr15:42750600-42756800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:42750600-42756800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:42750600-42756800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:42750600-42757200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:42750600-42757200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:42750600-42757200	Weak transcription	HUVEC	blood vessel
36	chr15:42750600-42757400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:42750600-42757400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:42750600-42757400	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:42750600-42757800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:42750600-42757800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:42750600-42760400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:42750600-42761400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:42750600-42761400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:42750600-42761800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr15:42750600-42763200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr15:42750600-42766800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr15:42750800-42756800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:42750800-42757200	Weak transcription	Brain Angular Gyrus	brain
49	chr15:42750800-42757400	Weak transcription	Brain Substantia Nigra	brain
50	chr15:42750800-42757400	Weak transcription	Left Ventricle	heart

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