Variant report

Variant	rs12349672
Chromosome Location	chr9:101010704-101010705
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100986946..100989189-chr9:101010558..101012631,2	MCF-7	breast:
2	chr9:100955094..100957753-chr9:101010315..101013161,2	MCF-7	breast:
3	chr9:100987323..100990186-chr9:101009264..101011823,2	K562	blood:
4	chr9:101010177..101013807-chr9:101023006..101027119,4	K562	blood:
5	chr9:100983664..100985681-chr9:101009334..101011944,2	MCF-7	breast:
6	chr9:101010134..101012336-chr9:101021281..101022782,2	K562	blood:
7	chr9:101010268..101015223-chr9:101016008..101021084,8	K562	blood:
8	chr9:100987323..100989657-chr9:101010085..101011823,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000095383	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10156520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10156596	0.82[EUR][1000 genomes]
rs10818728	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10985682	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10985714	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10985747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12339418	0.82[ASN][1000 genomes]
rs12341227	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12341228	0.80[ASN][1000 genomes]
rs12343605	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12347890	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12350177	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12551379	0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12551959	0.85[CEU][hapmap]
rs12552446	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12553553	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12683370	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12683816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685443	0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12685596	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12685597	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1435255	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs16914485	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2304391	0.85[CEU][hapmap]
rs28636819	0.82[AMR][1000 genomes]
rs41283620	0.86[ASN][1000 genomes]
rs55740603	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56397452	0.83[ASN][1000 genomes]
rs56406831	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7029612	0.85[YRI][hapmap]
rs7037857	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7853699	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9987447	0.93[AMR][1000 genomes]
rs9987773	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
2	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100968800-101011000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr9:100989600-101016000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:100991400-101015400	Weak transcription	Brain Anterior Caudate	brain
4	chr9:100991800-101011400	Weak transcription	Right Ventricle	heart
5	chr9:100992200-101012800	Weak transcription	Brain Substantia Nigra	brain
6	chr9:100992200-101016000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr9:100993400-101012600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:100995000-101016600	Weak transcription	Brain Angular Gyrus	brain
9	chr9:100995800-101011200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr9:100996000-101012400	Weak transcription	Fetal Stomach	stomach
11	chr9:100996000-101016000	Weak transcription	Pancreas	Pancrea
12	chr9:100996200-101017200	Weak transcription	Ovary	ovary
13	chr9:100996600-101011200	Weak transcription	Thymus	Thymus
14	chr9:100996800-101011000	Weak transcription	Liver	Liver
15	chr9:101003800-101011200	Weak transcription	Gastric	stomach
16	chr9:101004000-101011000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:101004200-101011000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:101004200-101015800	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:101004200-101017200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:101005200-101017200	Weak transcription	Brain Germinal Matrix	brain
21	chr9:101006400-101014000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr9:101006600-101014000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:101006600-101016600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:101006800-101011400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:101006800-101016800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:101007000-101013800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:101008000-101011000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:101008000-101012600	Weak transcription	HepG2	liver
29	chr9:101008400-101012400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:101008600-101010800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr9:101008800-101013600	Enhancers	Placenta	Placenta
32	chr9:101008800-101013800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr9:101009000-101017200	Weak transcription	Aorta	Aorta
34	chr9:101009200-101010800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr9:101009200-101011000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:101009200-101011200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr9:101009200-101015800	Weak transcription	Stomach Mucosa	stomach
38	chr9:101009200-101016600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr9:101009400-101012600	Enhancers	Primary hematopoietic stem cells	blood
40	chr9:101010200-101010800	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr9:101010200-101010800	Enhancers	K562	blood
42	chr9:101010200-101011200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:101010200-101011600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr9:101010200-101011800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr9:101010200-101011800	Flanking Active TSS	Hela-S3	cervix
46	chr9:101010200-101012000	Enhancers	HUVEC	blood vessel
47	chr9:101010200-101012000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr9:101010200-101012600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:101010200-101012600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr9:101010200-101013400	Genic enhancers	HMEC	breast

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