Variant report

Variant	rs12327994
Chromosome Location	chr2:172206486-172206487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10173812	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10195398	0.85[CHD][hapmap]
rs11674303	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685308	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11695531	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1178014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989804	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3731986	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3731987	0.87[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs6744452	0.94[ASW][hapmap];0.82[CEU][hapmap];0.88[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7349355	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs888521	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1003130	chr2:172189196-172237268	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12327994	WIPF1	cis	cerebellum	SCAN
rs12327994	CDCA7	cis	cerebellum	SCAN
rs12327994	SSB	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172171800-172211600	Weak transcription	Fetal Intestine Small	intestine
2	chr2:172172800-172222400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:172181000-172221600	Weak transcription	K562	blood
4	chr2:172193600-172218200	Weak transcription	HepG2	liver
5	chr2:172202200-172212200	Weak transcription	Esophagus	oesophagus
6	chr2:172202400-172211800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:172203400-172217200	Weak transcription	Small Intestine	intestine
8	chr2:172203800-172218600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:172204000-172213800	Weak transcription	Primary B cells from cord blood	blood
10	chr2:172204600-172218600	Weak transcription	Ovary	ovary
11	chr2:172204800-172211600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:172204800-172211800	Weak transcription	Fetal Stomach	stomach
13	chr2:172204800-172222400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:172205000-172207400	Weak transcription	NH-A	brain
15	chr2:172205000-172211800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:172205000-172212600	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:172205000-172213000	Weak transcription	A549	lung
18	chr2:172205000-172215200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:172205000-172216600	Weak transcription	Adipose Nuclei	Adipose
20	chr2:172205000-172217200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:172205000-172221400	Weak transcription	NHEK	skin
22	chr2:172205000-172221600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:172205000-172221800	Weak transcription	Osteobl	bone
24	chr2:172205000-172222400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:172205200-172211800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:172205200-172211800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:172205200-172218400	Weak transcription	Psoas Muscle	Psoas
28	chr2:172205200-172218400	Weak transcription	NHDF-Ad	bronchial
29	chr2:172205200-172221600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:172205200-172224000	Weak transcription	Colon Smooth Muscle	Colon

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