Variant report

Variant	rs140108
Chromosome Location	chr22:30130776-30130777
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	chr22:30122754..30125379-chr22:30128810..30131334,3	MCF-7	breast:
2	chr22:30124714..30127862-chr22:30128538..30131492,3	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1076137	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs131278	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs131291	0.83[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs131294	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs131296	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs140105	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs140125	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs140135	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs140142	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs140151	0.91[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes]
rs2349225	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes]
rs249400	0.84[EUR][1000 genomes]
rs36578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs3887275	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs3958025	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs4823063	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs5752968	0.91[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs140108	UCRC	Cis_1M	lymphoblastoid	RTeQTL

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	chr22:30123200-30131800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr22:30123200-30135800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr22:30123200-30137600	Weak transcription	Osteobl	bone
7	chr22:30123200-30142800	Weak transcription	Brain Substantia Nigra	brain
8	chr22:30123600-30133400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr22:30123600-30134000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr22:30123600-30135600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr22:30123600-30146800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:30123600-30147000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr22:30123800-30136600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr22:30124200-30131000	Strong transcription	Brain Germinal Matrix	brain
15	chr22:30124600-30133600	Weak transcription	Fetal Lung	lung
16	chr22:30124600-30136600	Weak transcription	Primary B cells from cord blood	blood
17	chr22:30124800-30135200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr22:30125000-30135600	Weak transcription	Dnd41	blood
19	chr22:30125200-30131600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr22:30125400-30146200	Weak transcription	NHLF	lung
21	chr22:30125600-30132400	Strong transcription	Lung	lung
22	chr22:30125800-30132400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr22:30126000-30144600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr22:30126200-30132200	Strong transcription	Thymus	Thymus
25	chr22:30126400-30130800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr22:30126400-30133800	Weak transcription	HSMMtube	muscle
27	chr22:30126600-30131400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr22:30126600-30145200	Strong transcription	Primary T cells from cord blood	blood
29	chr22:30126800-30131800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr22:30127400-30131800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr22:30127600-30133400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr22:30127600-30134400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr22:30127600-30140600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr22:30127800-30135400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr22:30127800-30137200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr22:30128200-30131000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr22:30128200-30133800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr22:30128200-30136200	Weak transcription	Small Intestine	intestine
39	chr22:30128400-30135600	Weak transcription	HepG2	liver
40	chr22:30128800-30131000	Enhancers	Primary hematopoietic stem cells	blood
41	chr22:30129000-30130800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr22:30129000-30131000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr22:30129000-30131200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr22:30129000-30131600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr22:30129000-30131800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr22:30129000-30132400	Strong transcription	Gastric	stomach
47	chr22:30129000-30139200	Strong transcription	Stomach Smooth Muscle	stomach
48	chr22:30129200-30130800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr22:30129400-30139000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr22:30129400-30144600	Strong transcription	Liver	Liver

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