Variant report

Variant	rs3911955
Chromosome Location	chr17:15431549-15431550
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10153259	0.89[JPT][hapmap]
rs12450262	0.83[ASN][1000 genomes]
rs12450302	0.83[ASN][1000 genomes]
rs12450921	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12451284	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12452965	0.83[ASN][1000 genomes]
rs12453059	0.81[ASN][1000 genomes]
rs12938444	0.83[ASN][1000 genomes]
rs12939314	0.89[JPT][hapmap]
rs12943480	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12948266	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12953212	0.83[ASN][1000 genomes]
rs16940991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17702522	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17702771	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2013835	0.83[ASN][1000 genomes]
rs2532479	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2654261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34236889	0.83[ASN][1000 genomes]
rs34453320	0.83[ASN][1000 genomes]
rs35078459	0.83[ASN][1000 genomes]
rs35406616	0.83[ASN][1000 genomes]
rs35448233	0.83[ASN][1000 genomes]
rs35699886	0.83[ASN][1000 genomes]
rs3852809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4054418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4791625	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4792619	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6502459	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6502462	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71367505	0.85[ASN][1000 genomes]
rs71367507	0.81[ASN][1000 genomes]
rs716388	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7226342	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7359507	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7359511	0.81[ASN][1000 genomes]
rs8064461	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8068610	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8070714	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8071082	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8074456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs917567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers 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	33 gene(s)	inside rSNPs	diseases
7	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv962260	chr17:15428362-15439978	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3911955	AC005517.3	cis	Thyroid	GTEx
rs3911955	CDRT4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15383400-15455000	Weak transcription	Gastric	stomach
2	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:15406800-15450600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:15416200-15466000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:15417600-15466400	Weak transcription	Ovary	ovary
7	chr17:15418600-15450600	Weak transcription	Brain Angular Gyrus	brain
8	chr17:15418800-15450600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr17:15419600-15442000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr17:15419800-15442400	Weak transcription	Thymus	Thymus
11	chr17:15419800-15448400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr17:15420000-15441800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr17:15420000-15442000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr17:15420000-15442000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr17:15420000-15442000	Weak transcription	A549	lung
16	chr17:15420000-15448400	Weak transcription	Placenta	Placenta
17	chr17:15420000-15450800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr17:15420200-15442000	Weak transcription	Lung	lung
19	chr17:15420200-15448600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr17:15420400-15435200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr17:15420400-15442000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:15420400-15442000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:15420400-15442000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr17:15420400-15452800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr17:15420600-15435600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr17:15420600-15441800	Weak transcription	Fetal Brain Female	brain
27	chr17:15420600-15442000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:15420600-15459600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr17:15420800-15442000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:15420800-15448200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr17:15420800-15448400	Weak transcription	Fetal Muscle Leg	muscle
32	chr17:15420800-15448400	Weak transcription	HSMM	muscle
33	chr17:15420800-15450200	Weak transcription	Brain Germinal Matrix	brain
34	chr17:15421200-15450800	Weak transcription	Fetal Kidney	kidney
35	chr17:15421200-15453000	Weak transcription	Aorta	Aorta
36	chr17:15421800-15435400	Weak transcription	HSMMtube	muscle
37	chr17:15421800-15465600	Weak transcription	Hela-S3	cervix
38	chr17:15422000-15435600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr17:15422200-15441800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr17:15422400-15441800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr17:15422400-15441800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr17:15422400-15442000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:15422400-15447000	Weak transcription	HepG2	liver
44	chr17:15422400-15448400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr17:15422600-15441600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr17:15422800-15441800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:15422800-15465800	Weak transcription	Fetal Intestine Small	intestine
48	chr17:15423000-15442000	Weak transcription	Fetal Stomach	stomach
49	chr17:15423000-15448400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr17:15423000-15451000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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