Variant report

Variant	rs2179367
Chromosome Location	chr6:149762537-149762538
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	chr6:149762143..149764363-chr6:149765543..149768268,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1074495	0.91[ASN][1000 genomes]
rs1934117	0.84[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2143076	0.84[CEU][hapmap];0.92[EUR][1000 genomes]
rs2153219	0.84[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2262617	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744430	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2789488	0.84[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2789492	0.93[EUR][1000 genomes]
rs2789493	0.91[ASN][1000 genomes]
rs2789495	0.90[ASN][1000 genomes]
rs2789501	0.81[JPT][hapmap]
rs372205	0.96[MEX][hapmap]
rs4895788	0.94[EUR][1000 genomes]
rs4895789	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4897124	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897125	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs504985	0.95[CEU][hapmap];0.93[TSI][hapmap]
rs506268	0.84[CEU][hapmap]
rs514839	0.95[CEU][hapmap];0.93[TSI][hapmap]
rs521845	0.95[CEU][hapmap];0.93[TSI][hapmap]
rs536203	0.95[CEU][hapmap]
rs537354	0.95[CEU][hapmap]
rs540538	0.95[CEU][hapmap]
rs556775	0.85[JPT][hapmap]
rs560051	0.95[CEU][hapmap]
rs562428	0.95[CEU][hapmap]
rs577001	0.95[CEU][hapmap]
rs585022	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs626755	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs632360	0.90[ASN][1000 genomes]
rs634440	0.90[ASN][1000 genomes]
rs638407	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs652807	0.95[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs656461	0.81[JPT][hapmap]
rs6570965	0.84[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap]
rs664951	0.84[ASN][1000 genomes]
rs760897	0.89[ASN][1000 genomes]
rs9285519	0.95[CEU][hapmap]
rs9322178	0.95[CEU][hapmap]
rs9373589	0.95[CEU][hapmap];0.93[TSI][hapmap]
rs9373592	0.90[EUR][1000 genomes]
rs9390677	0.95[CEU][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	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv5533	chr6:149748047-149793072	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv464076	chr6:149755695-149798835	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv604846	chr6:149755695-149798835	ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Dupuytren's disease	21732829	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2179367	RAET1E	cis	cerebellum	SCAN
rs2179367	LRP11	cis	parietal	SCAN
rs2179367	LRP11	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149749800-149764400	Weak transcription	Right Atrium	heart
2	chr6:149753400-149762800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:149753400-149770000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:149753600-149768400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:149753600-149769600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:149760600-149766600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr6:149760800-149765800	Weak transcription	GM12878-XiMat	blood
8	chr6:149761600-149769600	Weak transcription	Primary B cells from cord blood	blood
9	chr6:149761800-149762800	Enhancers	Fetal Thymus	thymus
10	chr6:149761800-149763200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:149761800-149763200	Enhancers	Fetal Intestine Small	intestine
12	chr6:149762000-149762600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:149762000-149762600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr6:149762000-149762800	Enhancers	Hela-S3	cervix
15	chr6:149762000-149763000	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr6:149762000-149763200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:149762000-149763200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:149762000-149763200	Enhancers	Fetal Intestine Large	intestine
19	chr6:149762000-149763200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr6:149762000-149763600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:149762200-149762600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:149762200-149762600	Flanking Bivalent TSS/Enh	HepG2	liver
23	chr6:149762200-149762600	Enhancers	NH-A	brain
24	chr6:149762200-149763000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:149762200-149763200	Enhancers	Ovary	ovary
26	chr6:149762400-149762600	Enhancers	Left Ventricle	heart
27	chr6:149762400-149762800	Enhancers	NHLF	lung
28	chr6:149762400-149763200	Enhancers	Fetal Lung	lung
29	chr6:149762400-149763200	Enhancers	Placenta	Placenta
30	chr6:149762400-149763200	Bivalent Enhancer	Fetal Stomach	stomach
31	chr6:149762400-149764600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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