Variant report

Variant	rs496157
Chromosome Location	chr6:149629326-149629327
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	chr6:149625453..149629470-chr6:149636058..149640474,5	MCF-7	breast:
2	chr6:149628297..149630405-chr6:149634848..149636468,2	K562	blood:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs477088	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs481651	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs482388	0.88[ASW][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[YRI][hapmap]
rs491576	0.86[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs492461	0.81[ASN][1000 genomes]
rs494228	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs496091	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs496124	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs497036	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs501651	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs508534	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs515295	0.86[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs517207	0.81[ASN][1000 genomes]
rs518836	0.80[EUR][1000 genomes]
rs527010	0.83[AFR][1000 genomes]
rs530516	0.88[ASW][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap]
rs534625	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs551983	0.82[EUR][1000 genomes]
rs555309	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs559055	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs559271	0.90[CEU][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs563373	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs567995	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs568054	0.84[EUR][1000 genomes]
rs571436	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs579488	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs583074	0.86[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs597144	0.86[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs610707	0.86[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs611550	0.86[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs612749	0.86[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs613276	0.86[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs625571	0.86[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs639289	0.81[ASN][1000 genomes]
rs642403	0.90[CEU][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs643491	0.90[JPT][hapmap]
rs643921	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs647043	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs657940	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs657941	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs676567	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs799389	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1015360	chr6:149609804-149649982	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv18913	chr6:149629115-149633318	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs496157	RAET1E	cis	cerebellum	SCAN
rs496157	LRP11	cis	cerebellum	SCAN
rs496157	VIP	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149628000-149629400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:149628000-149629400	Enhancers	Osteobl	bone
3	chr6:149628000-149637800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:149628200-149629400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:149628200-149629400	Enhancers	NH-A	brain
6	chr6:149628400-149629600	Enhancers	HSMM	muscle
7	chr6:149628600-149629400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:149628600-149629800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:149628600-149629800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:149628600-149631800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:149628600-149637200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:149628800-149629400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:149628800-149629400	Weak transcription	NHDF-Ad	bronchial
14	chr6:149628800-149629800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:149629200-149630000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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