Variant report

Variant	rs6557086
Chromosome Location	chr6:151033086-151033087
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	chr6:151032065..151034026-chr6:151038847..151040382,2	K562	blood:
2	chr6:151031833..151034692-chr6:151036440..151039323,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12207259	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869940	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6557084	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6557085	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769973	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9371193	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383542	0.85[TSI][hapmap]
rs9478788	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030326	chr6:150967665-151641372	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3439835	chr6:151027582-151036981	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1019919	chr6:151028969-151161789	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv538474	chr6:151028969-151161789	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6557086	SUMO4	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:151015200-151033200	Weak transcription	Right Atrium	heart
2	chr6:151019000-151033200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:151019000-151035200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:151021600-151040600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:151024200-151034200	Weak transcription	Right Ventricle	heart
6	chr6:151025600-151033200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:151026000-151033600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:151026800-151033200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:151026800-151043600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:151027000-151033200	Weak transcription	Fetal Intestine Small	intestine
11	chr6:151027400-151033200	Weak transcription	Fetal Kidney	kidney
12	chr6:151029200-151033200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:151029400-151033200	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:151029400-151033200	Weak transcription	Placenta	Placenta
15	chr6:151029400-151041800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:151029600-151033200	Weak transcription	Left Ventricle	heart
17	chr6:151029800-151033200	Strong transcription	Primary B cells from cord blood	blood
18	chr6:151030800-151034200	Enhancers	Stomach Mucosa	stomach
19	chr6:151031200-151033200	Weak transcription	Pancreas	Pancrea
20	chr6:151031200-151034200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr6:151031400-151033200	Weak transcription	NHEK	skin
22	chr6:151032000-151033200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:151032000-151033200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:151032200-151033200	Weak transcription	Colonic Mucosa	Colon
25	chr6:151032200-151033200	Weak transcription	Lung	lung
26	chr6:151032200-151037600	Weak transcription	Gastric	stomach
27	chr6:151032600-151033400	Genic enhancers	Thymus	Thymus
28	chr6:151032800-151033400	Enhancers	Esophagus	oesophagus
29	chr6:151032800-151034000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:151032800-151034000	Enhancers	Adipose Nuclei	Adipose
31	chr6:151032800-151034200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr6:151032800-151034400	Enhancers	Liver	Liver
33	chr6:151032800-151036600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr6:151033000-151033200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:151033000-151033600	Enhancers	Brain Anterior Caudate	brain
36	chr6:151033000-151033600	Enhancers	Fetal Stomach	stomach
37	chr6:151033000-151033800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:151033000-151034000	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr6:151033000-151034200	Enhancers	Duodenum Mucosa	Duodenum
40	chr6:151033000-151034200	Enhancers	Fetal Thymus	thymus
41	chr6:151033000-151034200	Enhancers	Small Intestine	intestine
42	chr6:151033000-151034200	Enhancers	HMEC	breast
43	chr6:151033000-151035000	Enhancers	Spleen	Spleen
44	chr6:151033000-151035200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:151033000-151035600	Enhancers	Fetal Lung	lung
46	chr6:151033000-151035800	Enhancers	Brain Substantia Nigra	brain
47	chr6:151033000-151035800	Enhancers	Fetal Heart	heart
48	chr6:151033000-151036200	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links