Variant report

Variant	rs4673317
Chromosome Location	chr2:206160453-206160454
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10804147	0.80[JPT][hapmap]
rs1207411	0.81[ASN][1000 genomes]
rs1207415	0.81[ASN][1000 genomes]
rs1207420	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1207421	0.89[ASN][1000 genomes]
rs1207424	0.87[ASN][1000 genomes]
rs1207426	0.91[ASN][1000 genomes]
rs1207428	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1207429	0.89[ASN][1000 genomes]
rs1207430	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1207431	0.91[ASN][1000 genomes]
rs1207432	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1207433	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1207434	0.82[ASN][1000 genomes]
rs1207435	0.84[ASN][1000 genomes]
rs1207436	0.84[ASN][1000 genomes]
rs1207437	0.84[ASN][1000 genomes]
rs1207438	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1207440	0.81[ASN][1000 genomes]
rs1207441	0.81[ASN][1000 genomes]
rs1211319	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1212609	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13024952	0.84[ASN][1000 genomes]
rs1861510	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1861511	0.94[ASN][1000 genomes]
rs1912845	0.80[JPT][hapmap]
rs2080418	0.80[JPT][hapmap]
rs2160453	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251539	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2541148	0.95[ASN][1000 genomes]
rs2541149	0.88[ASN][1000 genomes]
rs2541151	0.84[ASN][1000 genomes]
rs2541152	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2541153	0.84[ASN][1000 genomes]
rs2541154	0.84[ASN][1000 genomes]
rs2704638	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2704643	0.81[ASN][1000 genomes]
rs2704644	0.84[ASN][1000 genomes]
rs2878692	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4505506	0.80[JPT][hapmap]
rs4675512	0.86[ASN][1000 genomes]
rs62171496	0.84[ASN][1000 genomes]
rs849189	0.84[ASN][1000 genomes]
rs849193	0.82[ASN][1000 genomes]
rs849194	0.84[ASN][1000 genomes]
rs849216	0.82[ASN][1000 genomes]
rs849218	0.84[ASN][1000 genomes]
rs849219	0.84[ASN][1000 genomes]
rs849220	0.83[ASN][1000 genomes]
rs849221	0.84[ASN][1000 genomes]
rs849222	0.84[ASN][1000 genomes]
rs849223	0.84[ASN][1000 genomes]
rs849224	0.81[ASN][1000 genomes]
rs849250	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998485	chr2:205407813-206184006	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536122	chr2:205407813-206184006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1012780	chr2:206124954-206546271	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4673317	PARD3B	cis	cerebellum	SCAN
rs4673317	NDUFB3	cis	parietal	SCAN
rs4673317	ALS2CR12	cis	parietal	SCAN
rs4673317	CASP8	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:206097200-206170600	Weak transcription	HSMMtube	muscle
2	chr2:206138800-206162200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:206153000-206165800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:206154200-206168200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:206154600-206165800	Weak transcription	Ovary	ovary
6	chr2:206156000-206161000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:206157000-206167200	Weak transcription	Fetal Intestine Large	intestine
8	chr2:206157000-206170400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:206157000-206170800	Weak transcription	Aorta	Aorta
10	chr2:206157400-206169400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:206157400-206170800	Weak transcription	Pancreas	Pancrea
12	chr2:206158600-206166600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:206158800-206162000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:206159000-206161800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:206159200-206162000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:206159800-206161000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:206159800-206161800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:206160000-206169800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:206160200-206165600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:206160200-206169800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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