Variant report

Variant	rs140128
Chromosome Location	chr22:30150140-30150141
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	chr22:30149066..30150867-chr22:30154689..30156736,2	K562	blood:
2	chr22:30148345..30151530-chr22:30155464..30158156,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200976	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs105311	0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131260	0.96[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs131261	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs131262	0.96[CHB][hapmap];0.89[JPT][hapmap]
rs131263	0.92[ASN][1000 genomes]
rs131264	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131265	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131266	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131267	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131268	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131270	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131271	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs131272	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs131273	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs131274	0.90[ASN][1000 genomes]
rs131275	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs131277	0.96[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs131279	0.96[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs131281	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs131282	0.95[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs131284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs131285	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs131286	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs131287	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131298	0.88[EUR][1000 genomes]
rs131301	0.84[CHB][hapmap]
rs140094	0.89[JPT][hapmap]
rs140095	0.90[ASN][1000 genomes]
rs140096	0.96[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs140097	0.92[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs140099	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs140100	0.96[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs140101	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140102	0.96[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140103	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs140104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140107	0.96[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140110	0.96[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs140111	0.96[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs140113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140117	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs140118	0.96[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs140119	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140120	0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs140121	0.91[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140122	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140123	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140124	0.96[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140129	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140130	0.81[EUR][1000 genomes]
rs140131	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs140133	0.96[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs140134	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs140139	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs140140	0.85[EUR][1000 genomes]
rs140145	0.83[CHB][hapmap]
rs140149	0.83[CHB][hapmap]
rs2074706	0.84[CHB][hapmap]
rs2074707	0.84[CHB][hapmap]
rs249396	0.86[EUR][1000 genomes]
rs249397	0.85[EUR][1000 genomes]
rs249398	0.84[CHB][hapmap]
rs249401	0.83[EUR][1000 genomes]
rs36572	0.86[EUR][1000 genomes]
rs36576	0.83[CHB][hapmap]
rs5752961	0.84[CHB][hapmap]
rs5752962	0.86[EUR][1000 genomes]
rs5752964	0.83[CHB][hapmap]
rs5763512	0.84[CHB][hapmap]
rs5997530	0.84[CHB][hapmap]
rs713656	0.84[CHB][hapmap]
rs713657	0.84[CHB][hapmap]
rs740041	0.84[CHB][hapmap]
rs7954	0.86[EUR][1000 genomes]
rs81800	0.83[CHB][hapmap]
rs9306465	0.84[CHB][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	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	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs140128	MTMR3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30130200-30150200	Weak transcription	A549	lung
2	chr22:30130400-30150600	Strong transcription	Fetal Intestine Small	intestine
3	chr22:30131600-30162000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:30134400-30158400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr22:30136000-30154800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr22:30141200-30150800	Strong transcription	Fetal Brain Female	brain
7	chr22:30141600-30154200	Weak transcription	Osteobl	bone
8	chr22:30141800-30155400	Strong transcription	Fetal Stomach	stomach
9	chr22:30143600-30154200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr22:30144400-30161800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr22:30144400-30162000	Weak transcription	Placenta	Placenta
12	chr22:30144400-30162200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr22:30144600-30160000	Weak transcription	Dnd41	blood
14	chr22:30144600-30161800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr22:30144600-30161800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr22:30144600-30161800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr22:30144600-30162000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr22:30144800-30155000	Weak transcription	Ovary	ovary
19	chr22:30144800-30161800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr22:30144800-30161800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr22:30144800-30161800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr22:30145000-30150200	Weak transcription	HSMMtube	muscle
23	chr22:30145200-30154000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr22:30145400-30154200	Weak transcription	NHDF-Ad	bronchial
25	chr22:30146000-30150800	Strong transcription	Primary T cells from cord blood	blood
26	chr22:30146000-30161800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr22:30146400-30155000	Weak transcription	Brain Substantia Nigra	brain
28	chr22:30146600-30154800	Weak transcription	Left Ventricle	heart
29	chr22:30146600-30161800	Weak transcription	Brain Germinal Matrix	brain
30	chr22:30146800-30151800	Weak transcription	Esophagus	oesophagus
31	chr22:30146800-30151800	Weak transcription	NHLF	lung
32	chr22:30146800-30153400	Weak transcription	Aorta	Aorta
33	chr22:30146800-30154800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr22:30146800-30161800	Weak transcription	Brain Anterior Caudate	brain
35	chr22:30146800-30161800	Weak transcription	Right Ventricle	heart
36	chr22:30147000-30162000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr22:30147000-30162200	Weak transcription	Gastric	stomach
38	chr22:30147400-30152200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr22:30147400-30154000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr22:30147400-30160200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr22:30147400-30160200	Weak transcription	HepG2	liver
42	chr22:30147400-30161800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr22:30147600-30161800	Weak transcription	Primary B cells from cord blood	blood
44	chr22:30147600-30161800	Weak transcription	NHEK	skin
45	chr22:30147600-30162200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr22:30147800-30150400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr22:30147800-30150800	Weak transcription	GM12878-XiMat	blood
48	chr22:30147800-30153600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr22:30147800-30160200	Weak transcription	Fetal Thymus	thymus
50	chr22:30147800-30160800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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