Variant report

Variant	rs338887
Chromosome Location	chr5:145144419-145144420
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10038598	0.85[CEU][hapmap]
rs10041421	0.85[CEU][hapmap]
rs1019925	0.85[CEU][hapmap]
rs1019926	0.85[CEU][hapmap]
rs12651915	0.92[ASN][1000 genomes]
rs13158196	0.92[ASN][1000 genomes]
rs1821250	0.89[TSI][hapmap]
rs1897545	0.89[TSI][hapmap]
rs1972778	0.85[CEU][hapmap]
rs2400198	0.85[CEU][hapmap]
rs338884	0.92[CEU][hapmap]
rs338888	0.84[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs338889	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs338893	0.89[TSI][hapmap]
rs338894	0.92[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs338895	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs338896	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4305683	0.85[TSI][hapmap]
rs4358578	0.92[ASN][1000 genomes]
rs4422574	0.92[ASN][1000 genomes]
rs4587127	0.92[ASN][1000 genomes]
rs4913037	0.92[ASN][1000 genomes]
rs582130	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587224	0.89[TSI][hapmap]
rs627623	0.92[ASN][1000 genomes]
rs677498	0.89[TSI][hapmap]
rs6869743	0.92[ASN][1000 genomes]
rs6871384	0.92[ASN][1000 genomes]
rs6875843	0.92[ASN][1000 genomes]
rs7717605	0.92[ASN][1000 genomes]
rs7734685	0.86[EUR][1000 genomes]
rs7735617	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021851	chr5:145106686-145187560	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs338887	SPINK1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145105400-145179000	Weak transcription	Pancreas	Pancrea
2	chr5:145109400-145194400	Weak transcription	Colonic Mucosa	Colon
3	chr5:145111400-145166800	Weak transcription	K562	blood
4	chr5:145114000-145163400	Weak transcription	Small Intestine	intestine
5	chr5:145124200-145145000	Weak transcription	Fetal Intestine Small	intestine
6	chr5:145126800-145155000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:145130600-145146800	Weak transcription	Adipose Nuclei	Adipose
8	chr5:145131000-145156800	Weak transcription	Gastric	stomach
9	chr5:145133000-145154800	Weak transcription	Fetal Lung	lung
10	chr5:145133400-145145200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:145133800-145146800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:145133800-145154600	Weak transcription	Osteobl	bone
13	chr5:145134400-145146800	Weak transcription	Lung	lung
14	chr5:145134800-145147000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:145135400-145146600	Weak transcription	Aorta	Aorta
16	chr5:145137800-145154400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:145138000-145157800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:145138200-145146800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr5:145139000-145165400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:145139600-145145200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:145140000-145146800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr5:145140000-145157800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:145140400-145157200	Weak transcription	Left Ventricle	heart
24	chr5:145140600-145153800	Weak transcription	Ovary	ovary
25	chr5:145140600-145156000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:145141200-145146400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:145141200-145194400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:145141400-145148600	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:145141600-145146200	Weak transcription	Liver	Liver
30	chr5:145141600-145155600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:145142000-145144600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:145142000-145145400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:145142400-145147400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr5:145142400-145162400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:145142600-145146800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:145143600-145144800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:145143800-145145400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr5:145144000-145144800	Weak transcription	Fetal Stomach	stomach
39	chr5:145144200-145146600	Weak transcription	Fetal Intestine Large	intestine
40	chr5:145144200-145149800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr5:145144200-145155200	Weak transcription	HUVEC	blood vessel
42	chr5:145144200-145156800	Weak transcription	Right Ventricle	heart
43	chr5:145144400-145144600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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