Variant report

Variant	rs17462966
Chromosome Location	chr22:30133579-30133580
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	chr22:30130941..30133818-chr22:30144985..30147499,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs131269	0.99[ASN][1000 genomes]
rs131289	0.85[ASN][1000 genomes]
rs140147	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs2301402	0.86[CHB][hapmap]
rs3788417	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73161005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	nsv914963	chr22:30075052-30133579	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv914964	chr22:30081715-30150549	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv515720	chr22:30081715-30163526	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv914966	chr22:30088442-30138548	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1065072	chr22:30102176-30155245	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv914967	chr22:30103476-30133579	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17462966	TTC28	cis	cerebellum	SCAN
rs17462966	THOC5	cis	lung	GTEx
rs17462966	CRYBB3	cis	parietal	SCAN
rs17462966	THOC5	cis	Artery Tibial	GTEx
rs17462966	NEFH	cis	cerebellum	SCAN
rs17462966	NIPSNAP1	cis	cerebellum	SCAN
rs17462966	ASCC2	cis	cerebellum	SCAN
rs17462966	CABP7	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30117000-30137200	Weak transcription	HSMM	muscle
2	chr22:30117200-30133800	Weak transcription	Right Atrium	heart
3	chr22:30123000-30135400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr22:30123200-30135800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr22:30123200-30137600	Weak transcription	Osteobl	bone
6	chr22:30123200-30142800	Weak transcription	Brain Substantia Nigra	brain
7	chr22:30123600-30134000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr22:30123600-30135600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr22:30123600-30146800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:30123600-30147000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr22:30123800-30136600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr22:30124600-30133600	Weak transcription	Fetal Lung	lung
13	chr22:30124600-30136600	Weak transcription	Primary B cells from cord blood	blood
14	chr22:30124800-30135200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr22:30125000-30135600	Weak transcription	Dnd41	blood
16	chr22:30125400-30146200	Weak transcription	NHLF	lung
17	chr22:30126000-30144600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr22:30126400-30133800	Weak transcription	HSMMtube	muscle
19	chr22:30126600-30145200	Strong transcription	Primary T cells from cord blood	blood
20	chr22:30127600-30134400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr22:30127600-30140600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr22:30127800-30135400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr22:30127800-30137200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr22:30128200-30133800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr22:30128200-30136200	Weak transcription	Small Intestine	intestine
26	chr22:30128400-30135600	Weak transcription	HepG2	liver
27	chr22:30129000-30139200	Strong transcription	Stomach Smooth Muscle	stomach
28	chr22:30129400-30139000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr22:30129400-30144600	Strong transcription	Liver	Liver
30	chr22:30129800-30138600	Strong transcription	Left Ventricle	heart
31	chr22:30129800-30141000	Strong transcription	Fetal Stomach	stomach
32	chr22:30130000-30133800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr22:30130000-30133800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr22:30130000-30135000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr22:30130000-30135200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr22:30130000-30135600	Weak transcription	Brain Angular Gyrus	brain
37	chr22:30130000-30141000	Weak transcription	Colon Smooth Muscle	Colon
38	chr22:30130200-30134000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr22:30130200-30135000	Weak transcription	Colonic Mucosa	Colon
40	chr22:30130200-30135400	Weak transcription	Brain Anterior Caudate	brain
41	chr22:30130200-30150200	Weak transcription	A549	lung
42	chr22:30130400-30133600	Weak transcription	Aorta	Aorta
43	chr22:30130400-30135400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr22:30130400-30150600	Strong transcription	Fetal Intestine Small	intestine
45	chr22:30130600-30140200	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr22:30130600-30149800	Weak transcription	Psoas Muscle	Psoas
47	chr22:30130800-30134200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr22:30130800-30135000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr22:30130800-30135600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr22:30130800-30138000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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