Variant report

Variant	rs13019331
Chromosome Location	chr2:173467301-173467302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1010752	0.81[ASN][1000 genomes]
rs10181851	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1075638	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10930561	0.93[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10930562	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930563	0.83[ASN][1000 genomes]
rs10930565	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1097478	0.83[ASN][1000 genomes]
rs1133602	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11891127	0.83[AFR][1000 genomes]
rs11904158	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];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11904366	0.80[TSI][hapmap]
rs12476204	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12613307	0.80[CHB][hapmap]
rs12693008	0.89[ASN][1000 genomes]
rs13015260	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13024563	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13385403	0.84[LWK][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs13401676	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13417334	0.80[TSI][hapmap]
rs1530864	0.93[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs1530865	0.93[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs1531150	0.85[ASN][1000 genomes]
rs16860693	0.93[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs16860696	0.83[YRI][hapmap]
rs16860697	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs16860737	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16860741	0.93[ASN][1000 genomes]
rs17702263	0.80[TSI][hapmap]
rs1868901	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1869923	0.90[ASN][1000 genomes]
rs2290563	0.84[CEU][hapmap]
rs2290564	0.83[AFR][1000 genomes]
rs2599260	0.90[ASN][1000 genomes]
rs2599261	0.90[ASN][1000 genomes]
rs2599262	0.90[ASN][1000 genomes]
rs2599263	0.90[ASN][1000 genomes]
rs2599264	0.90[ASN][1000 genomes]
rs2599265	0.90[ASN][1000 genomes]
rs2599266	0.90[ASN][1000 genomes]
rs2606062	0.90[ASN][1000 genomes]
rs2606063	0.90[ASN][1000 genomes]
rs2606064	0.89[ASN][1000 genomes]
rs2606065	0.90[ASN][1000 genomes]
rs2606066	0.90[ASN][1000 genomes]
rs2606067	0.90[ASN][1000 genomes]
rs2606070	0.90[ASN][1000 genomes]
rs34051646	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35892983	0.91[ASN][1000 genomes]
rs3765065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769321	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61505737	0.87[ASN][1000 genomes]
rs62167835	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66460331	0.82[AFR][1000 genomes]
rs6710129	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6723872	0.83[LWK][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs6731354	0.82[ASN][1000 genomes]
rs6733679	0.90[ASN][1000 genomes]
rs6738196	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6752257	0.80[TSI][hapmap];0.80[YRI][hapmap]
rs6752386	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs70937083	0.87[ASN][1000 genomes]
rs70937084	0.87[ASN][1000 genomes]
rs7584769	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8179584	0.86[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs836590	0.90[ASN][1000 genomes]
rs836608	0.84[ASN][1000 genomes]
rs836614	0.84[ASN][1000 genomes]
rs836616	0.84[ASN][1000 genomes]
rs836617	0.84[ASN][1000 genomes]
rs836629	0.90[ASN][1000 genomes]
rs836630	0.90[ASN][1000 genomes]
rs836631	0.90[ASN][1000 genomes]
rs836634	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv875415	chr2:173444462-173501069	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv875416	chr2:173444462-173504674	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv875417	chr2:173460803-173501069	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv875418	chr2:173460803-173504674	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13019331	CYBRD1	cis	parietal	SCAN
rs13019331	ZAK	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173431400-173480600	Weak transcription	Gastric	stomach
2	chr2:173440200-173467600	Weak transcription	NH-A	brain
3	chr2:173443200-173472200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:173444200-173470400	Weak transcription	Psoas Muscle	Psoas
5	chr2:173444400-173480200	Strong transcription	HepG2	liver
6	chr2:173445400-173471000	Weak transcription	Brain Substantia Nigra	brain
7	chr2:173451800-173471800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:173452000-173479800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:173452400-173469400	Weak transcription	Lung	lung
10	chr2:173452800-173478000	Weak transcription	Fetal Brain Male	brain
11	chr2:173452800-173478600	Weak transcription	Spleen	Spleen
12	chr2:173453800-173472400	Weak transcription	Brain Angular Gyrus	brain
13	chr2:173453800-173478600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:173454000-173471600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:173454200-173475200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:173454400-173477800	Weak transcription	Pancreas	Pancrea
17	chr2:173454400-173479800	Weak transcription	Esophagus	oesophagus
18	chr2:173454400-173489000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:173454600-173477800	Weak transcription	NHLF	lung
20	chr2:173454800-173475200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:173454800-173477800	Weak transcription	Colonic Mucosa	Colon
22	chr2:173454800-173488200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:173455200-173480200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:173455400-173478400	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:173457000-173469000	Strong transcription	Primary B cells from peripheral blood	blood
26	chr2:173457200-173480000	Strong transcription	Dnd41	blood
27	chr2:173460400-173468000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:173460800-173479000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:173461200-173472200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:173461400-173488800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:173461400-173504200	Weak transcription	NHEK	skin
32	chr2:173461800-173470400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:173461800-173470800	Weak transcription	NHDF-Ad	bronchial
34	chr2:173462200-173467400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:173462200-173469600	Weak transcription	Osteobl	bone
36	chr2:173462200-173470600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:173462200-173474800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:173462200-173476600	Weak transcription	Fetal Stomach	stomach
39	chr2:173462200-173477400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:173462200-173477800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:173462200-173477800	Weak transcription	Placenta	Placenta
42	chr2:173462200-173478600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:173462200-173479600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:173462200-173481200	Weak transcription	Brain Anterior Caudate	brain
45	chr2:173462200-173481400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:173462200-173507400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:173462400-173469800	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:173462400-173470800	Weak transcription	Adipose Nuclei	Adipose
49	chr2:173462400-173471000	Weak transcription	Aorta	Aorta
50	chr2:173462400-173475400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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