Variant report

Variant	rs10912675
Chromosome Location	chr1:171227216-171227217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10798304	0.84[EUR][1000 genomes]
rs10798305	0.85[EUR][1000 genomes]
rs10912694	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10912749	0.84[EUR][1000 genomes]
rs16864258	0.83[JPT][hapmap]
rs2284129	0.86[CEU][hapmap]
rs6660565	0.84[EUR][1000 genomes]
rs7412314	0.81[EUR][1000 genomes]
rs7877	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]

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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10912675	FMO4	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171221000-171227600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:171221200-171228200	Enhancers	Fetal Intestine Large	intestine
3	chr1:171222000-171227400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:171224800-171227400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:171224800-171227800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:171225000-171227600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:171225000-171228000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:171226000-171227400	Enhancers	Duodenum Mucosa	Duodenum
9	chr1:171226000-171228000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:171226000-171228600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:171226000-171228800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:171226000-171228800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:171226000-171228800	Enhancers	NHEK	skin
14	chr1:171226000-171229200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:171226200-171227800	Enhancers	Fetal Heart	heart
16	chr1:171226200-171228800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:171226200-171229200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr1:171226400-171227400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:171226400-171228200	Enhancers	Fetal Stomach	stomach
20	chr1:171226400-171228600	Enhancers	Adipose Nuclei	Adipose
21	chr1:171226400-171229200	Enhancers	Ovary	ovary
22	chr1:171226600-171227400	Enhancers	Esophagus	oesophagus
23	chr1:171226600-171227400	Enhancers	Lung	lung
24	chr1:171226600-171228200	Flanking Active TSS	Fetal Muscle Trunk	muscle
25	chr1:171226600-171228600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:171226600-171229200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:171226600-171229200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:171226800-171227800	Weak transcription	Right Atrium	heart
29	chr1:171226800-171228000	Weak transcription	Fetal Kidney	kidney
30	chr1:171226800-171228200	Active TSS	Stomach Smooth Muscle	stomach
31	chr1:171226800-171228600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr1:171226800-171228800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:171227000-171227400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:171227000-171227600	Weak transcription	Fetal Thymus	thymus
35	chr1:171227000-171227800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:171227200-171227400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr1:171227200-171227600	Weak transcription	Placenta	Placenta
38	chr1:171227200-171228200	Flanking Active TSS	Fetal Muscle Leg	muscle
39	chr1:171227200-171228200	Weak transcription	HMEC	breast
40	chr1:171227200-171228600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:171227200-171228600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr1:171227200-171228600	Genic enhancers	Fetal Intestine Small	intestine
43	chr1:171227200-171228600	Enhancers	Fetal Lung	lung
44	chr1:171227200-171229000	Enhancers	H1 Cell Line	embryonic stem cell

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