Variant report

Variant	rs13223151
Chromosome Location	chr7:129129740-129129741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:129123425..129125126-chr7:129129619..129131299,2	MCF-7	breast:
2	chr7:129128173..129130689-chr7:129136182..129137829,2	K562	blood:
3	chr7:129128271..129130546-chr7:129249994..129251580,2	K562	blood:
4	chr7:129127657..129130703-chr7:129131027..129133692,4	K562	blood:

Variant related genes	Relation type
ENSG00000106459	Chromatin interaction
ENSG00000199846	Chromatin interaction
ENSG00000273329	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11762085	1.00[CHB][hapmap];0.90[MKK][hapmap];1.00[ASN][1000 genomes]
rs11768409	1.00[ASN][1000 genomes]
rs11769581	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771549	1.00[JPT][hapmap]
rs11771705	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771841	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772187	0.89[ASN][1000 genomes]
rs13221695	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221778	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241869	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13243857	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247598	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1348750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349402	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[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526897	0.89[ASN][1000 genomes]
rs1562291	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17552411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs17552570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs17552854	0.85[GIH][hapmap]
rs17553578	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628726	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402952	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34275118	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34440172	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911743	1.00[ASN][1000 genomes]
rs35084372	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35191983	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35294314	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35312667	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35886223	0.89[ASN][1000 genomes]
rs36064596	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36086855	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62479481	1.00[ASN][1000 genomes]
rs62479487	1.00[ASN][1000 genomes]
rs62480621	0.89[ASN][1000 genomes]
rs62480623	0.89[ASN][1000 genomes]
rs62480628	0.89[ASN][1000 genomes]
rs62480631	0.89[ASN][1000 genomes]
rs62489087	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62489113	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62489119	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62489121	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657664	1.00[CHD][hapmap]
rs68047560	1.00[ASN][1000 genomes]
rs6958637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs6971551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs6974105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977752	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7781018	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785864	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7805214	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896158	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];0.95[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv831128	chr7:129063040-129240800	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13223151	FAM40B	cis	cerebellum	SCAN
rs13223151	LOC407835	cis	cerebellum	SCAN
rs13223151	AHCYL2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129093400-129134800	Weak transcription	Right Atrium	heart
2	chr7:129103000-129141200	Weak transcription	Hela-S3	cervix
3	chr7:129103200-129135400	Weak transcription	HepG2	liver
4	chr7:129104200-129141600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:129112200-129134600	Weak transcription	Fetal Heart	heart
6	chr7:129120800-129130000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:129121200-129130800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:129121600-129129800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:129121600-129132600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:129122000-129141800	Weak transcription	Right Ventricle	heart
11	chr7:129124000-129137200	Weak transcription	Esophagus	oesophagus
12	chr7:129124400-129132000	Weak transcription	Psoas Muscle	Psoas
13	chr7:129126000-129129800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:129126000-129129800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr7:129126000-129131200	Weak transcription	Left Ventricle	heart
16	chr7:129126000-129133400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:129126000-129136600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:129126200-129133000	Weak transcription	NHEK	skin
19	chr7:129126400-129133000	Weak transcription	Brain Anterior Caudate	brain
20	chr7:129127000-129130000	Strong transcription	K562	blood
21	chr7:129127800-129133400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:129128000-129133400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:129128000-129133800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:129128600-129130000	Enhancers	Osteobl	bone
25	chr7:129128800-129129800	Enhancers	HSMMtube	muscle
26	chr7:129128800-129130000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr7:129128800-129130000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:129128800-129130000	Enhancers	NHLF	lung
29	chr7:129128800-129130200	Enhancers	HSMM	muscle
30	chr7:129129000-129129800	Enhancers	NHDF-Ad	bronchial
31	chr7:129129400-129129800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:129129400-129130000	Enhancers	NH-A	brain
33	chr7:129129400-129133000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr7:129129400-129133200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr7:129129400-129141800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:129129600-129133000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:129129600-129133000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:129129600-129133400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr7:129129600-129133600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:129129600-129135800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:129129600-129141000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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