Variant report

Variant	rs6006220
Chromosome Location	chr22:30051433-30051434
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	chr22:30050125..30052733-chr22:30083134..30085567,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1008515	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs10483155	0.91[JPT][hapmap]
rs16987752	0.86[JPT][hapmap]
rs2072303	0.86[JPT][hapmap]
rs2074947	0.86[JPT][hapmap]
rs2074949	0.86[JPT][hapmap]
rs2074950	0.86[JPT][hapmap]
rs2267146	0.86[JPT][hapmap]
rs2267149	0.91[JPT][hapmap]
rs2270079	0.86[JPT][hapmap]
rs2302140	0.86[JPT][hapmap]
rs2302142	0.86[JPT][hapmap]
rs2530678	0.83[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2530680	0.84[CHD][hapmap];0.82[JPT][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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6006220	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs6006220	C22orf13	cis	parietal	SCAN
rs6006220	C22orf36	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:30020200-30057000	Weak transcription	Psoas Muscle	Psoas
4	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
5	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
6	chr22:30022200-30053400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr22:30026800-30055800	Weak transcription	Gastric	stomach
8	chr22:30027600-30057200	Weak transcription	Brain Hippocampus Middle	brain
9	chr22:30027800-30056000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr22:30029600-30053800	Weak transcription	Esophagus	oesophagus
11	chr22:30032200-30057000	Weak transcription	Colonic Mucosa	Colon
12	chr22:30032200-30070000	Weak transcription	Fetal Brain Male	brain
13	chr22:30033000-30053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:30034400-30060400	Weak transcription	K562	blood
15	chr22:30035400-30060800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr22:30035600-30057200	Weak transcription	Placenta	Placenta
17	chr22:30036600-30052000	Weak transcription	Brain Anterior Caudate	brain
18	chr22:30036800-30053000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr22:30037200-30064200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr22:30038200-30057000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr22:30038400-30055800	Weak transcription	Fetal Kidney	kidney
22	chr22:30038400-30060600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr22:30038800-30057000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr22:30038800-30069800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr22:30039000-30053800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr22:30039000-30054000	Weak transcription	Colon Smooth Muscle	Colon
27	chr22:30039000-30054600	Weak transcription	Aorta	Aorta
28	chr22:30039000-30054800	Weak transcription	NHLF	lung
29	chr22:30039000-30068000	Weak transcription	Hela-S3	cervix
30	chr22:30039200-30053800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr22:30039200-30056200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr22:30041800-30054000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr22:30042200-30057200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr22:30042400-30052600	Weak transcription	GM12878-XiMat	blood
35	chr22:30042400-30052800	Weak transcription	Primary B cells from cord blood	blood
36	chr22:30042400-30053000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr22:30043800-30064000	Weak transcription	Fetal Heart	heart
38	chr22:30044800-30053600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr22:30044800-30058200	Weak transcription	Right Ventricle	heart
40	chr22:30044800-30059600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr22:30045000-30053400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr22:30045000-30053400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr22:30045000-30053800	Weak transcription	Fetal Intestine Large	intestine
44	chr22:30045000-30060600	Weak transcription	Brain Substantia Nigra	brain
45	chr22:30045400-30053000	Weak transcription	Fetal Lung	lung
46	chr22:30045400-30053400	Weak transcription	HSMMtube	muscle
47	chr22:30045400-30053600	Weak transcription	Ovary	ovary
48	chr22:30045600-30054000	Weak transcription	Pancreas	Pancrea
49	chr22:30047000-30053000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr22:30047400-30052200	Strong transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links