Variant report

Variant	rs1934117
Chromosome Location	chr6:149754677-149754678
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149749225..149751406-chr6:149752259..149754784,2	K562	blood:
2	chr6:149398184..149404330-chr6:149748783..149757211,17	MCF-7	breast:
3	chr6:149352390..149354385-chr6:149752598..149755216,2	MCF-7	breast:
4	chr6:149351119..149355583-chr6:149748923..149756337,13	MCF-7	breast:
5	chr6:149379587..149381868-chr6:149752319..149755254,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1001242	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1074495	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1339185	0.82[EUR][1000 genomes]
rs2007062	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2153219	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179367	0.90[ASN][1000 genomes]
rs2262617	0.90[ASN][1000 genomes]
rs237005	0.82[MEX][hapmap]
rs2789493	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789495	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789496	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2789498	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2789501	0.84[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs3765290	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs475681	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4895789	0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4897124	0.88[ASN][1000 genomes]
rs4897125	0.85[ASN][1000 genomes]
rs512685	0.81[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs556775	0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs587155	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62441728	0.82[EUR][1000 genomes]
rs626755	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs632360	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs634440	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656461	0.89[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs664951	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs760897	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805027	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs909793	0.81[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs9377218	0.81[CEU][hapmap];0.91[EUR][1000 genomes]

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	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	nsv517606	chr6:149744632-149755695	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1934117	SUMO4	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149746800-149762000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:149749800-149764400	Weak transcription	Right Atrium	heart
3	chr6:149753400-149756800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:149753400-149762200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:149753400-149762800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:149753400-149770000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:149753600-149754800	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:149753600-149755000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:149753600-149755400	Weak transcription	Fetal Lung	lung
10	chr6:149753600-149755400	Weak transcription	Ovary	ovary
11	chr6:149753600-149758200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:149753600-149762200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:149753600-149768400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:149753600-149769600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:149753800-149754800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:149753800-149754800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:149753800-149754800	Weak transcription	HSMMtube	muscle
18	chr6:149753800-149755800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:149753800-149755800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:149753800-149755800	Enhancers	Osteobl	bone
21	chr6:149754400-149761800	Weak transcription	Fetal Thymus	thymus

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