Variant report

Variant	rs909793
Chromosome Location	chr6:149753599-149753600
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149736139..149738247-chr6:149750968..149753957,2	K562	blood:
2	chr6:149748430..149751387-chr6:149751741..149754089,3	MCF-7	breast:
3	chr6:149749225..149751406-chr6:149752259..149754784,2	K562	blood:
4	chr6:149398184..149404330-chr6:149748783..149757211,17	MCF-7	breast:
5	chr6:149350092..149350652-chr6:149752991..149753790,4	MCF-7	breast:
6	chr6:149403286..149404899-chr6:149752639..149753736,6	MCF-7	breast:
7	chr10:123366642..123368236-chr6:149751907..149753798,2	MCF-7	breast:
8	chr6:149352390..149354385-chr6:149752598..149755216,2	MCF-7	breast:
9	chr6:149364299..149365300-chr6:149752858..149754111,6	K562	blood:
10	chr6:149517097..149517616-chr6:149753109..149753764,2	K562	blood:
11	chr6:149347837..149348431-chr6:149752868..149753657,2	MCF-7	breast:
12	chr6:149748841..149750725-chr6:149751621..149753759,2	K562	blood:
13	chr6:149403053..149404232-chr6:149752839..149753842,8	K562	blood:
14	chr6:149511094..149511659-chr6:149753092..149753721,3	MCF-7	breast:
15	chr6:149335068..149337695-chr6:149751708..149753851,2	MCF-7	breast:
16	chr6:149351119..149355583-chr6:149748923..149756337,13	MCF-7	breast:
17	chr6:149379587..149381868-chr6:149752319..149755254,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1001242	0.95[EUR][1000 genomes]
rs1074495	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1339185	0.88[EUR][1000 genomes]
rs17086451	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1934117	0.81[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2007062	0.88[EUR][1000 genomes]
rs2143076	0.81[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2153219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2341783	0.87[JPT][hapmap]
rs2341784	0.87[JPT][hapmap]
rs2744427	0.87[JPT][hapmap]
rs2744431	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2744433	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2744434	0.87[JPT][hapmap];0.80[AMR][1000 genomes]
rs2789487	0.80[AMR][1000 genomes]
rs2789488	0.90[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2789489	0.80[AMR][1000 genomes]
rs2789490	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2789492	0.91[ASN][1000 genomes]
rs2789493	0.82[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2789495	0.99[EUR][1000 genomes]
rs2789496	0.95[EUR][1000 genomes]
rs2789498	0.95[EUR][1000 genomes]
rs2789500	0.87[JPT][hapmap]
rs2789501	0.90[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs3734296	0.87[JPT][hapmap]
rs3765290	0.94[EUR][1000 genomes]
rs4360154	0.80[AMR][1000 genomes]
rs472810	0.81[JPT][hapmap]
rs474369	0.87[JPT][hapmap]
rs475681	0.92[EUR][1000 genomes]
rs478767	0.87[JPT][hapmap]
rs480526	0.86[JPT][hapmap]
rs480778	0.80[AMR][1000 genomes]
rs4895788	0.91[ASN][1000 genomes]
rs4897117	0.80[AMR][1000 genomes]
rs492956	0.90[JPT][hapmap]
rs494340	0.82[JPT][hapmap]
rs501926	0.87[JPT][hapmap]
rs504762	0.82[JPT][hapmap]
rs504985	0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs506268	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs511105	0.87[JPT][hapmap]
rs512685	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs513923	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs514839	0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs515133	0.83[JPT][hapmap]
rs521845	0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs527971	0.83[JPT][hapmap]
rs532250	0.83[JPT][hapmap]
rs536203	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs537354	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs538386	0.87[JPT][hapmap]
rs540538	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs556335	0.87[JPT][hapmap]
rs556775	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs559052	0.86[JPT][hapmap]
rs560051	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs562428	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs565825	0.86[JPT][hapmap]
rs570442	0.82[JPT][hapmap]
rs577001	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs579789	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs587155	0.95[EUR][1000 genomes]
rs588028	0.80[AMR][1000 genomes]
rs60006373	0.80[ASN][1000 genomes]
rs600739	0.81[JPT][hapmap]
rs62441728	0.88[EUR][1000 genomes]
rs626755	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs632360	0.82[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs634440	0.99[EUR][1000 genomes]
rs638407	0.81[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs641068	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs652514	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs652807	0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs652921	0.87[JPT][hapmap];0.80[AMR][1000 genomes]
rs656461	1.00[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs6570965	0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs663625	0.87[JPT][hapmap]
rs664951	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs674919	0.83[ASW][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs760897	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs805027	0.83[EUR][1000 genomes]
rs9285519	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs9322178	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs9373589	0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs9373592	0.86[ASN][1000 genomes]
rs9377216	0.80[AMR][1000 genomes]
rs9377217	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9377218	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390676	0.86[JPT][hapmap]
rs9390677	0.90[JPT][hapmap]
rs9399686	0.80[AMR][1000 genomes]
rs9404034	0.87[JPT][hapmap]
rs9404037	0.82[AMR][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
rs909793	SUMO4	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

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	chr6:149752800-149753600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:149752800-149753600	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr6:149752800-149753600	Enhancers	Liver	Liver
6	chr6:149752800-149754400	Enhancers	Fetal Thymus	thymus
7	chr6:149753000-149753600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr6:149753000-149753600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:149753000-149753600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:149753000-149753600	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:149753000-149753600	Enhancers	Primary T cells from cord blood	blood
12	chr6:149753000-149753600	Enhancers	Primary hematopoietic stem cells	blood
13	chr6:149753000-149753600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr6:149753000-149753600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:149753000-149753600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:149753000-149753600	Bivalent Enhancer	Adipose Nuclei	Adipose
17	chr6:149753000-149753600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:149753000-149753600	Enhancers	Brain Substantia Nigra	brain
19	chr6:149753000-149753600	Enhancers	Fetal Intestine Large	intestine
20	chr6:149753000-149753600	Enhancers	Fetal Lung	lung
21	chr6:149753000-149753600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr6:149753000-149753600	Enhancers	Fetal Muscle Leg	muscle
23	chr6:149753000-149753600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr6:149753000-149753600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:149753000-149753600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr6:149753000-149753600	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr6:149753000-149753600	Flanking Active TSS	HSMM	muscle
28	chr6:149753000-149753600	Enhancers	NH-A	brain
29	chr6:149753000-149753800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:149753000-149753800	Active TSS	Brain Angular Gyrus	brain
31	chr6:149753000-149753800	Enhancers	Fetal Heart	heart
32	chr6:149753000-149753800	Enhancers	Placenta	Placenta
33	chr6:149753000-149753800	Enhancers	HepG2	liver
34	chr6:149753000-149753800	Flanking Active TSS	Osteobl	bone
35	chr6:149753200-149753600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:149753200-149753600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr6:149753200-149753600	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr6:149753200-149753600	Enhancers	Lung	lung
39	chr6:149753200-149753600	Enhancers	Ovary	ovary
40	chr6:149753200-149753600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr6:149753200-149753600	Enhancers	Hela-S3	cervix
42	chr6:149753400-149753600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:149753400-149753600	Enhancers	Primary T cells fromperipheralblood	blood
44	chr6:149753400-149753600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:149753400-149753600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr6:149753400-149753600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr6:149753400-149753600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:149753400-149753600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr6:149753400-149753600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:149753400-149753600	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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