Variant report

Variant	rs2938171
Chromosome Location	chr17:15449627-15449628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs189330	0.88[ASN][1000 genomes]
rs190206	0.85[ASN][1000 genomes]
rs2270136	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236804	0.82[ASN][1000 genomes]
rs236809	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs236810	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs2906970	0.84[ASW][hapmap]
rs2907502	0.91[ASN][1000 genomes]
rs2907505	0.85[ASN][1000 genomes]
rs2938158	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2938170	0.86[ASN][1000 genomes]
rs2954739	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2954742	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	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
6	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
7	nsv960418	chr17:15441505-15470653	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3434808	chr17:15444327-15450925	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
9	esv3395445	chr17:15444877-15459575	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv457695	chr17:15447364-15611495	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv574462	chr17:15447364-15611495	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2938171	CDRT4	cis	parietal	SCAN
rs2938171	TEKT3	cis	cerebellum	SCAN
rs2938171	TEKT3	cis	parietal	SCAN
rs2938171	TRIM16	cis	parietal	SCAN
rs2938171	CDRT4	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

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	chr17:15420000-15450800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:15420400-15452800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:15420600-15459600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr17:15420800-15450200	Weak transcription	Brain Germinal Matrix	brain
13	chr17:15421200-15450800	Weak transcription	Fetal Kidney	kidney
14	chr17:15421200-15453000	Weak transcription	Aorta	Aorta
15	chr17:15421800-15465600	Weak transcription	Hela-S3	cervix
16	chr17:15422800-15465800	Weak transcription	Fetal Intestine Small	intestine
17	chr17:15423000-15451000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr17:15429400-15450400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr17:15429800-15450400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr17:15429800-15466000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:15429800-15466400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr17:15431000-15465400	Weak transcription	K562	blood
23	chr17:15433800-15450600	Weak transcription	Brain Hippocampus Middle	brain
24	chr17:15437200-15450400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:15438800-15450400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr17:15439000-15466000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr17:15439600-15450200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr17:15439600-15456000	Weak transcription	Colon Smooth Muscle	Colon
29	chr17:15439600-15466000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr17:15439800-15466400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr17:15440000-15450800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr17:15440200-15466400	Weak transcription	Left Ventricle	heart
33	chr17:15440600-15451000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:15440800-15450400	Weak transcription	Psoas Muscle	Psoas
35	chr17:15440800-15466000	Weak transcription	NHEK	skin
36	chr17:15441000-15449800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr17:15441000-15466000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr17:15442600-15450200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr17:15442600-15450400	Weak transcription	Spleen	Spleen
40	chr17:15442600-15450600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr17:15442600-15450600	Weak transcription	Fetal Brain Female	brain
42	chr17:15442600-15465400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr17:15442600-15466000	Weak transcription	A549	lung
44	chr17:15442600-15466400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr17:15442800-15450000	Weak transcription	Small Intestine	intestine
46	chr17:15442800-15450400	Weak transcription	Fetal Stomach	stomach
47	chr17:15442800-15462600	Weak transcription	Thymus	Thymus
48	chr17:15442800-15465800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr17:15442800-15466400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr17:15442800-15466400	Weak transcription	Lung	lung

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