Variant report

Variant	rs31452
Chromosome Location	chr5:16929983-16929984
allele	A/G
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:45)

rs_ID	r²[population]
rs13354237	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2016972	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2016983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2016997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2170642	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2217341	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2434960	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs2434962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2434965	0.81[EUR][1000 genomes]
rs2449479	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2454879	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs249137	0.83[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs249138	0.84[ASN][1000 genomes]
rs2562351	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2562361	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2562362	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2562363	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2562364	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2562365	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2562366	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2562367	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2625177	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2625178	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2625179	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2625180	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2625181	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2625182	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2625183	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2625184	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2625185	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2625186	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2625187	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2625188	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2625191	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2650457	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2650458	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2650459	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2650461	0.81[AMR][1000 genomes]
rs2650462	0.80[AMR][1000 genomes]
rs29453	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs29455	0.82[CHB][hapmap]
rs31453	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31464	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40984	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs922881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
3	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv3485757	chr5:16856475-16966851	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	esv3485758	chr5:16856475-16966851	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs31452	DSTYK	trans	brain	seeQTL
rs31452	MAP3K9	trans	brain	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16902200-16930000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:16904400-16933200	Weak transcription	Fetal Stomach	stomach
3	chr5:16914000-16931600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:16914000-16933200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:16914200-16930200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:16914600-16934400	Weak transcription	Psoas Muscle	Psoas
7	chr5:16916000-16930800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:16918400-16930400	Weak transcription	HSMMtube	muscle
9	chr5:16918600-16930400	Weak transcription	HSMM	muscle
10	chr5:16918600-16930600	Weak transcription	NH-A	brain
11	chr5:16919200-16930000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:16919200-16931600	Weak transcription	HMEC	breast
13	chr5:16920800-16930800	Weak transcription	Fetal Kidney	kidney
14	chr5:16922000-16930200	Weak transcription	NHDF-Ad	bronchial
15	chr5:16922000-16930600	Weak transcription	NHLF	lung
16	chr5:16922000-16931400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:16922000-16931600	Weak transcription	Osteobl	bone
18	chr5:16923200-16930800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:16923200-16932400	Weak transcription	Gastric	stomach
20	chr5:16924400-16930800	Weak transcription	Lung	lung
21	chr5:16924600-16930200	Weak transcription	Fetal Intestine Large	intestine
22	chr5:16924600-16931600	Weak transcription	Fetal Intestine Small	intestine
23	chr5:16924800-16930000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:16924800-16930200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:16924800-16930600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr5:16924800-16930600	Weak transcription	Small Intestine	intestine
27	chr5:16925000-16930200	Weak transcription	Fetal Muscle Leg	muscle
28	chr5:16926000-16930200	Weak transcription	Ovary	ovary
29	chr5:16926200-16933200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:16926600-16930000	Weak transcription	HUVEC	blood vessel
31	chr5:16926800-16930200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:16926800-16930600	Weak transcription	Spleen	Spleen
33	chr5:16927200-16930200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:16928200-16930200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:16928200-16930400	Weak transcription	NHEK	skin
36	chr5:16928200-16931600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:16928600-16930400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:16929400-16930200	Genic enhancers	A549	lung
39	chr5:16929400-16930600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:16929600-16930200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:16929600-16930800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:16929600-16933400	Enhancers	Stomach Mucosa	stomach
43	chr5:16929600-16933600	Enhancers	Pancreas	Pancrea
44	chr5:16929800-16930200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:16929800-16931000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:16929800-16933200	Enhancers	Fetal Lung	lung
47	chr5:16929800-16933800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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