Variant report

Variant	rs233940
Chromosome Location	chr6:132319670-132319671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	6:132269655-132282174..6:132317980-132319790	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000118523	Chromatin interaction
ENSG00000227220	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11154658	0.92[CHB][hapmap]
rs11154660	0.92[CHB][hapmap]
rs11154661	0.92[CHB][hapmap]
rs12200142	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12202220	0.92[CHB][hapmap]
rs12207504	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13212375	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2027035	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs233911	0.83[ASN][1000 genomes]
rs233917	0.86[ASN][1000 genomes]
rs233919	0.86[ASN][1000 genomes]
rs233923	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233925	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233944	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233947	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914192	0.92[CHB][hapmap]
rs6916800	0.92[CHB][hapmap]
rs7752454	0.92[CHB][hapmap]
rs7754913	0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv7968	chr6:131917172-132321099	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv470861	chr6:132291785-132351866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv886672	chr6:132299748-132349215	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv886673	chr6:132299748-132363507	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv427768	chr6:132300468-132398477	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv970350	chr6:132317890-132327515	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs233940	RPS12	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132303000-132320600	Weak transcription	Left Ventricle	heart
2	chr6:132304800-132320600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:132306200-132319800	Weak transcription	HSMM	muscle
4	chr6:132306200-132321400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:132317600-132324400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:132317800-132319800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:132317800-132320600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:132318000-132319800	Enhancers	Fetal Intestine Large	intestine
9	chr6:132318000-132320600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:132318200-132320000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:132318600-132320000	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr6:132318600-132320800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:132318800-132320000	Enhancers	A549	lung
14	chr6:132318800-132320800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:132318800-132324800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:132319200-132319800	Weak transcription	Aorta	Aorta
17	chr6:132319200-132320000	Weak transcription	Fetal Stomach	stomach
18	chr6:132319200-132320400	Enhancers	HepG2	liver
19	chr6:132319200-132320800	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr6:132319400-132319800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:132319400-132321800	Enhancers	Fetal Heart	heart
22	chr6:132319600-132320800	Enhancers	HSMMtube	muscle

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