Variant report

Variant	rs6900068
Chromosome Location	chr6:36879464-36879465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36877418..36880214-chr6:36894760..36897203,2	K562	blood:
2	chr6:36878376..36882517-chr6:36952548..36956029,4	MCF-7	breast:
3	chr6:36874669..36878220-chr6:36879029..36882017,3	MCF-7	breast:
4	chr6:36879267..36882648-chr6:36885620..36888336,3	K562	blood:
5	chr6:36841357..36843245-chr6:36878241..36882187,3	K562	blood:

Variant related genes	Relation type
ENSG00000137168	Chromatin interaction
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11751790	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs11754437	0.83[ASN][1000 genomes]
rs11756425	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs11758600	0.85[ASN][1000 genomes]
rs2071822	0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap]
rs2071823	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2293394	0.98[ASN][1000 genomes]
rs236346	0.82[YRI][hapmap]
rs4711472	0.85[ASN][1000 genomes]
rs4714019	0.82[ASN][1000 genomes]
rs4714020	0.84[CHB][hapmap]
rs6910582	0.85[ASN][1000 genomes]
rs6912602	0.82[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6913047	0.83[ASN][1000 genomes]
rs72846083	0.85[ASN][1000 genomes]
rs9357230	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs9368965	0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs9380614	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs9380625	0.92[ASN][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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6900068	PI16	cis	cerebellum	SCAN
rs6900068	PI16	cis	parietal	SCAN
rs6900068	C6orf89	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36854200-36881000	Weak transcription	Gastric	stomach
2	chr6:36854200-36887400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:36854400-36893000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:36854800-36881000	Weak transcription	A549	lung
5	chr6:36854800-36882000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:36854800-36884600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:36855400-36881000	Weak transcription	Small Intestine	intestine
8	chr6:36864600-36881200	Strong transcription	Fetal Intestine Small	intestine
9	chr6:36866200-36896400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:36866800-36881600	Strong transcription	Fetal Intestine Large	intestine
11	chr6:36867000-36897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:36868600-36882000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:36869800-36881400	Strong transcription	HepG2	liver
14	chr6:36870600-36882000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:36870600-36882000	Weak transcription	Fetal Kidney	kidney
16	chr6:36870800-36889400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:36871000-36879800	Weak transcription	HMEC	breast
18	chr6:36871000-36888400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:36871200-36882000	Weak transcription	Hela-S3	cervix
20	chr6:36872800-36879800	Weak transcription	HSMMtube	muscle
21	chr6:36873200-36881000	Weak transcription	Colonic Mucosa	Colon
22	chr6:36873400-36880200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:36873400-36880400	Weak transcription	Lung	lung
24	chr6:36874000-36879600	Weak transcription	NHLF	lung
25	chr6:36874000-36879800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:36874000-36879800	Weak transcription	Osteobl	bone
27	chr6:36874000-36882000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:36874800-36880800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:36875600-36879800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr6:36875600-36879800	Weak transcription	NH-A	brain
31	chr6:36875800-36879600	Weak transcription	Brain Germinal Matrix	brain
32	chr6:36875800-36880000	Weak transcription	Fetal Brain Male	brain
33	chr6:36875800-36881000	Weak transcription	Esophagus	oesophagus
34	chr6:36875800-36881000	Weak transcription	Stomach Mucosa	stomach
35	chr6:36876000-36879800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:36876000-36880400	Weak transcription	Aorta	Aorta
37	chr6:36876000-36885000	Strong transcription	Fetal Stomach	stomach
38	chr6:36876200-36879600	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:36876200-36879600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:36876200-36879800	Weak transcription	Spleen	Spleen
41	chr6:36876200-36880600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:36876200-36885800	Weak transcription	Psoas Muscle	Psoas
43	chr6:36876600-36879800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:36876600-36879800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:36876800-36879600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:36876800-36879600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:36876800-36879600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:36876800-36879800	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:36876800-36879800	Weak transcription	Left Ventricle	heart
50	chr6:36876800-36879800	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links