Variant report

Variant	rs1572226
Chromosome Location	chr6:118635079-118635080
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	chr6:118632785..118635288-chr6:118642370..118644781,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11153730	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11758375	0.94[CHB][hapmap];0.86[CHD][hapmap];0.88[YRI][hapmap]
rs11758402	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11968293	0.92[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]
rs12212582	0.88[CHB][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs1334489	0.89[AMR][1000 genomes]
rs1690662	0.83[ASN][1000 genomes]
rs188181	0.89[ASN][1000 genomes]
rs2065021	0.88[ASN][1000 genomes]
rs2093369	0.89[AMR][1000 genomes]
rs281861	0.88[CHB][hapmap]
rs281867	0.88[CHB][hapmap]
rs281868	0.81[CHB][hapmap]
rs283040	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs283042	0.88[CHB][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs283044	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs283045	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs283046	0.88[CHB][hapmap];0.81[MEX][hapmap]
rs283049	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs283050	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs283057	0.88[ASN][1000 genomes]
rs283062	0.88[CHB][hapmap];0.85[MEX][hapmap];0.89[ASN][1000 genomes]
rs283066	0.89[ASN][1000 genomes]
rs283077	0.81[CHB][hapmap]
rs283081	0.81[CHB][hapmap]
rs283082	0.81[CHB][hapmap]
rs283084	0.81[CHB][hapmap]
rs283085	0.81[CHB][hapmap]
rs283086	0.81[CHB][hapmap]
rs283088	0.81[CHB][hapmap]
rs283091	0.81[CHB][hapmap]
rs369383	0.86[ASN][1000 genomes]
rs372237	0.88[CHB][hapmap]
rs376875	0.88[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs387945	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs397445	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs399844	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs414091	0.82[ASN][1000 genomes]
rs419592	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs422268	0.86[ASN][1000 genomes]
rs422833	0.81[CHB][hapmap]
rs4294041	0.88[ASN][1000 genomes]
rs4307206	0.84[MEX][hapmap]
rs431115	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs445099	0.86[ASN][1000 genomes]
rs445566	0.88[CHB][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs447193	0.81[CHB][hapmap]
rs4946333	0.81[CHB][hapmap]
rs4946336	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs6906332	0.89[AMR][1000 genomes]
rs6911035	0.89[AMR][1000 genomes]
rs6911339	0.89[AMR][1000 genomes]
rs6927800	0.94[CHB][hapmap];0.88[YRI][hapmap]
rs6940985	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72967533	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs731695	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[YRI][hapmap]
rs7452622	0.93[CHB][hapmap]
rs7749263	0.94[CHB][hapmap];0.88[YRI][hapmap]
rs7772845	0.89[AMR][1000 genomes]
rs89107	0.81[CHB][hapmap]
rs927348	0.94[CHB][hapmap];0.88[YRI][hapmap]
rs9401060	0.81[CHB][hapmap]
rs9489327	0.94[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv604554	chr6:118631282-118716318	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv830787	chr6:118631902-118805106	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1572226	C6orf204	cis	cerebellum	SCAN
rs1572226	SLC35F1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118627800-118638000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:118627800-118641000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:118629000-118640800	Weak transcription	Fetal Brain Female	brain
4	chr6:118629200-118635200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:118629200-118640600	Weak transcription	Ovary	ovary
6	chr6:118629200-118641000	Weak transcription	Brain Angular Gyrus	brain
7	chr6:118629400-118640600	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:118630600-118640800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:118631400-118638800	Weak transcription	Brain Germinal Matrix	brain
10	chr6:118631400-118640600	Weak transcription	Psoas Muscle	Psoas
11	chr6:118631600-118635200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:118631600-118637000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:118631600-118638800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:118633000-118635200	Weak transcription	Aorta	Aorta
15	chr6:118633400-118635600	Enhancers	Fetal Heart	heart
16	chr6:118634000-118635600	Enhancers	Rectal Smooth Muscle	rectum
17	chr6:118634400-118642600	Enhancers	Colon Smooth Muscle	Colon
18	chr6:118634800-118638000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:118635000-118635400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:118635000-118635400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:118635000-118635400	Enhancers	Right Ventricle	heart
22	chr6:118635000-118635600	Genic enhancers	Left Ventricle	heart

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