Variant report

Variant	rs430008
Chromosome Location	chr3:155412344-155412345
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155406669..155408242-chr3:155411925..155413754,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs13076587	0.82[JPT][hapmap]
rs13079863	0.85[JPT][hapmap]
rs13089059	0.82[JPT][hapmap]
rs16825324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs173369	0.80[MEX][hapmap]
rs183088	0.80[MEX][hapmap]
rs1835212	0.81[GIH][hapmap]
rs1879090	0.82[JPT][hapmap]
rs1879091	0.82[JPT][hapmap]
rs2435194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680881	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2680882	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs358704	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs358706	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358707	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358708	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358711	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358712	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358896	0.82[JPT][hapmap]
rs358899	0.82[JPT][hapmap]
rs358902	0.82[JPT][hapmap]
rs358903	0.82[JPT][hapmap]
rs358905	0.82[JPT][hapmap]
rs358911	0.82[JPT][hapmap]
rs358912	0.82[JPT][hapmap]
rs358913	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs370157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378905	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386867	0.82[JPT][hapmap]
rs387885	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs392521	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393081	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394419	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394440	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs397231	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs402201	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs407212	0.81[ASN][1000 genomes]
rs407217	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412002	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs412664	0.91[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs414126	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs421072	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426069	0.83[ASN][1000 genomes]
rs429143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446716	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs447359	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs447751	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs448062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6777741	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7428196	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7644902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645831	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]

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	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs430008	PLCH1	cis	cerebellum	SCAN
rs430008	RARRES1	cis	cerebellum	SCAN
rs430008	SLC33A1	cis	parietal	SCAN
rs430008	SLC33A1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155395000-155416800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:155399800-155422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:155400600-155421000	Weak transcription	Fetal Intestine Small	intestine
4	chr3:155400800-155418400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:155408400-155413400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:155408800-155416400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:155408800-155418600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:155409000-155419200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:155409000-155419400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:155409200-155418400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:155409200-155422200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:155411000-155414000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:155411000-155420600	Weak transcription	Fetal Intestine Large	intestine
14	chr3:155412000-155412400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:155412000-155412800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:155412000-155414000	Enhancers	Cortex derived primary cultured neurospheres	brain

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