Variant report

Variant	rs134609
Chromosome Location	chr22:29475583-29475584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29472899..29476008-chr22:29545567..29548841,3	K562	blood:
2	chr22:29473028..29475906-chr22:29476306..29479164,3	K562	blood:
3	chr22:29467048..29472637-chr22:29472832..29480427,12	K562	blood:
4	chr22:29473632..29476528-chr22:29480609..29483295,2	K562	blood:
5	chr22:29468759..29472308-chr22:29473685..29477058,4	MCF-7	breast:
6	chr22:29473292..29476167-chr22:29497836..29499455,2	K562	blood:

Variant related genes	Relation type
ENSG00000183762	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs134561	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs134567	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs134569	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs134579	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs134592	0.97[GIH][hapmap]
rs134594	0.83[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs134596	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs134599	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs134600	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs134601	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs134602	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs134603	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs134604	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs134605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs134607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134613	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs134619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134620	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134621	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134625	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134626	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134630	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134632	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134635	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134636	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs134637	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134645	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134653	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs134657	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs134666	0.89[GIH][hapmap]
rs20037	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2049939	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713861	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs783	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv524259	chr22:29467221-29482221	Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs134609	KREMEN1	cis	Heart Left Ventricle	GTEx
rs134609	MORC2	cis	cerebellum	SCAN
rs134609	SRRD	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29470000-29477600	Weak transcription	Aorta	Aorta
2	chr22:29470400-29476400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:29470400-29485800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr22:29470600-29476200	Weak transcription	Psoas Muscle	Psoas
5	chr22:29470600-29478400	Weak transcription	Gastric	stomach
6	chr22:29470600-29478400	Weak transcription	Pancreas	Pancrea
7	chr22:29470800-29475600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr22:29470800-29476200	Weak transcription	Liver	Liver
9	chr22:29471000-29476200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr22:29471200-29476200	Weak transcription	Brain Anterior Caudate	brain
11	chr22:29471400-29476000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr22:29471400-29476200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr22:29471400-29488000	Weak transcription	Right Ventricle	heart
14	chr22:29471800-29477000	Enhancers	Fetal Thymus	thymus
15	chr22:29472200-29476400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr22:29472200-29477600	Weak transcription	HepG2	liver
17	chr22:29472400-29489000	Weak transcription	Fetal Intestine Small	intestine
18	chr22:29473200-29475600	Enhancers	Fetal Muscle Trunk	muscle
19	chr22:29473200-29481000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr22:29473400-29477600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr22:29474000-29475600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr22:29474000-29475600	Enhancers	Spleen	Spleen
23	chr22:29474000-29476600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr22:29474000-29476800	Enhancers	HSMMtube	muscle
25	chr22:29474000-29478000	Enhancers	NHDF-Ad	bronchial
26	chr22:29474000-29481400	Enhancers	Fetal Lung	lung
27	chr22:29474200-29477800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr22:29474200-29478800	Enhancers	Fetal Brain Female	brain
29	chr22:29474600-29476200	Enhancers	Colonic Mucosa	Colon
30	chr22:29474800-29475600	Enhancers	Lung	lung
31	chr22:29474800-29475600	Enhancers	Small Intestine	intestine
32	chr22:29474800-29475600	Enhancers	Stomach Mucosa	stomach
33	chr22:29474800-29476600	Enhancers	Fetal Kidney	kidney
34	chr22:29474800-29476800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr22:29474800-29476800	Enhancers	Placenta	Placenta
36	chr22:29474800-29477000	Enhancers	Right Atrium	heart
37	chr22:29474800-29478200	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr22:29474800-29478800	Enhancers	Hela-S3	cervix
39	chr22:29474800-29480400	Enhancers	Fetal Brain Male	brain
40	chr22:29474800-29480600	Enhancers	Ovary	ovary
41	chr22:29475000-29475600	Enhancers	Brain Cingulate Gyrus	brain
42	chr22:29475000-29475600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr22:29475000-29475800	Enhancers	Brain Hippocampus Middle	brain
44	chr22:29475000-29476000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr22:29475000-29476000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr22:29475000-29476600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr22:29475000-29476800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr22:29475000-29476800	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr22:29475000-29489200	Weak transcription	Fetal Intestine Large	intestine
50	chr22:29475200-29475600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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