Variant report

Variant	rs10130652
Chromosome Location	chr14:71953577-71953578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10129301	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10143346	0.85[ASN][1000 genomes]
rs10147863	0.87[YRI][hapmap]
rs11627930	0.82[ASN][1000 genomes]
rs11628525	0.80[MEX][hapmap];0.90[TSI][hapmap]
rs12878009	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12897119	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12897977	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs193440	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs193441	0.80[EUR][1000 genomes]
rs2041330	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2108048	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3088206	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36528	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36532	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36535	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41218	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41219	0.82[EUR][1000 genomes]
rs41225	0.83[EUR][1000 genomes]
rs41227	0.81[EUR][1000 genomes]
rs41229	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4464023	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4899396	0.83[EUR][1000 genomes]
rs4902939	0.81[ASN][1000 genomes]
rs7141155	0.82[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap]
rs7145435	0.92[CEU][hapmap];0.80[CHB][hapmap];0.95[YRI][hapmap]
rs7153726	0.87[EUR][1000 genomes]
rs7154208	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8007271	0.82[EUR][1000 genomes]
rs8007521	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8016217	0.92[CEU][hapmap];0.88[TSI][hapmap]
rs8023058	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs917391	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498021	chr14:71874708-72128721	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10130652	SLC8A3	cis	cerebellum	SCAN
rs10130652	VSX2	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71929200-71964200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr14:71930200-71954200	Weak transcription	Gastric	stomach
3	chr14:71930200-71955600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr14:71935400-71980400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr14:71939000-71959800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr14:71939200-71955800	Weak transcription	NHLF	lung
7	chr14:71939800-71954200	Weak transcription	Small Intestine	intestine
8	chr14:71941200-71954200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:71941200-71954400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr14:71941400-71954200	Weak transcription	HMEC	breast
11	chr14:71941400-71954600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr14:71941600-71954600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr14:71941600-71955400	Weak transcription	HSMMtube	muscle
14	chr14:71942000-71954600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr14:71942000-71964200	Weak transcription	Hela-S3	cervix
16	chr14:71943000-71955400	Weak transcription	HSMM	muscle
17	chr14:71945800-71956200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr14:71945800-71956400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr14:71946000-71954200	Weak transcription	NHEK	skin
20	chr14:71946000-71954800	Weak transcription	Fetal Muscle Leg	muscle
21	chr14:71946000-71959800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr14:71946000-71963200	Weak transcription	Dnd41	blood
23	chr14:71946000-71995600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr14:71947000-71964600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr14:71948200-71953800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr14:71948200-71958600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr14:71948800-71953800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr14:71949000-71953600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr14:71949000-71953800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr14:71949000-71955400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr14:71949000-71955600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr14:71949200-71954800	Weak transcription	Fetal Intestine Small	intestine
33	chr14:71949200-71958600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:71949400-71954000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr14:71950400-71958800	Weak transcription	Fetal Kidney	kidney
36	chr14:71950600-71958000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr14:71950800-71953800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr14:71950800-71953800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr14:71950800-71953800	Weak transcription	Spleen	Spleen
40	chr14:71950800-71954000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr14:71950800-71954200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr14:71950800-71954200	Weak transcription	Fetal Stomach	stomach
43	chr14:71950800-71954600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr14:71950800-71954800	Weak transcription	Fetal Intestine Large	intestine
45	chr14:71950800-71955600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr14:71950800-71958200	Weak transcription	Ovary	ovary
47	chr14:71950800-71958600	Weak transcription	Lung	lung
48	chr14:71951000-71953800	Weak transcription	Primary T cells from cord blood	blood
49	chr14:71951000-71956200	Enhancers	Fetal Lung	lung
50	chr14:71951800-71955800	Weak transcription	Primary B cells from peripheral blood	blood

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