Variant report

Variant	rs3789870
Chromosome Location	chr9:117835276-117835277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10759753	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13321	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1411456	0.95[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1411461	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1537017	0.95[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1547691	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs16932078	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2009023	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2104772	0.83[JPT][hapmap]
rs2210108	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789872	0.95[CEU][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes]
rs3789873	1.00[CEU][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes]
rs4460459	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs7027148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030164	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7032224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944223	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs944226	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs955450	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
3	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:117817800-117850600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:117819800-117848000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:117821400-117840200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:117822400-117854400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:117825400-117848000	Weak transcription	Lung	lung
9	chr9:117826400-117835800	Weak transcription	Aorta	Aorta
10	chr9:117826600-117835600	Weak transcription	HMEC	breast
11	chr9:117826800-117849400	Strong transcription	Osteobl	bone
12	chr9:117827000-117848600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr9:117827000-117849200	Strong transcription	NHDF-Ad	bronchial
14	chr9:117827200-117835800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:117827200-117855200	Strong transcription	NH-A	brain
16	chr9:117827400-117849200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:117829400-117839200	Strong transcription	NHLF	lung
18	chr9:117829800-117838400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:117830400-117840800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:117830800-117838600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:117831800-117848000	Strong transcription	Stomach Smooth Muscle	stomach
22	chr9:117832400-117835600	Strong transcription	NHEK	skin
23	chr9:117832400-117838600	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:117832400-117840600	Strong transcription	Fetal Stomach	stomach
25	chr9:117832400-117842400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:117832600-117839000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:117832800-117838600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:117833200-117835800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:117833400-117835800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:117833800-117836200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:117833800-117840400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:117834000-117849400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:117834000-117849800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:117834200-117840400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr9:117834200-117842000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr9:117834400-117837000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:117834400-117837000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:117834400-117839000	Strong transcription	Fetal Muscle Leg	muscle
39	chr9:117834600-117838200	Weak transcription	Fetal Intestine Large	intestine
40	chr9:117834600-117838600	Weak transcription	Esophagus	oesophagus
41	chr9:117834600-117839000	Strong transcription	Colon Smooth Muscle	Colon
42	chr9:117834800-117836400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:117834800-117840600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:117834800-117848600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:117835000-117835800	Weak transcription	Fetal Lung	lung
46	chr9:117835000-117836400	Strong transcription	Rectal Smooth Muscle	rectum
47	chr9:117835000-117840200	Weak transcription	Fetal Kidney	kidney
48	chr9:117835000-117842400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr9:117835200-117840400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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