Variant report

Variant	rs7974375
Chromosome Location	chr12:118585698-118585699
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118581884..118587240-chr12:118588010..118590251,5	K562	blood:
2	chr12:118582911..118584770-chr12:118584900..118587466,2	MCF-7	breast:
3	chr12:118581014..118583408-chr12:118584160..118586129,2	K562	blood:
4	chr12:118585664..118587231-chr12:118640737..118643618,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10507286	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1051077	1.00[ASN][1000 genomes]
rs12820035	1.00[CHB][hapmap]
rs16939761	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16948193	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16948197	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs16948204	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs16948230	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs16948234	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs17440315	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440336	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440364	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs17440433	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs17440669	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17440774	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17512142	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17512177	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17512198	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs17512219	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17512407	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17512483	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17512525	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2784	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs61943523	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943524	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943525	1.00[ASN][1000 genomes]
rs61943528	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294498	0.80[TSI][hapmap]
rs7302387	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7303417	1.00[JPT][hapmap]
rs7307393	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7309671	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7314987	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs73220119	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961312	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7962185	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7965350	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7980093	1.00[JPT][hapmap]
rs9943819	0.80[TSI][hapmap]

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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1054703	chr12:118575000-118638613	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv541611	chr12:118575000-118638613	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7974375	SUDS3	cis	parietal	SCAN
rs7974375	SUDS3	cis	cerebellum	SCAN
rs7974375	POP5	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118575200-118585800	Weak transcription	Fetal Heart	heart
2	chr12:118575400-118590400	Strong transcription	Fetal Muscle Trunk	muscle
3	chr12:118575400-118590600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:118575400-118590600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:118575400-118591400	Strong transcription	Fetal Stomach	stomach
6	chr12:118575600-118586800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:118575600-118588200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:118575600-118601600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:118575800-118587800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:118575800-118589200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:118575800-118590400	Strong transcription	Lung	lung
12	chr12:118575800-118590600	Strong transcription	Fetal Muscle Leg	muscle
13	chr12:118575800-118590800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr12:118576000-118586800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:118576000-118587200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:118576000-118591600	Strong transcription	Fetal Intestine Large	intestine
17	chr12:118576000-118591600	Strong transcription	Dnd41	blood
18	chr12:118576000-118601200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:118576000-118619600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:118576000-118624000	Weak transcription	Stomach Mucosa	stomach
21	chr12:118576200-118586600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:118576200-118587600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:118576200-118590400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:118576200-118590600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:118576200-118591000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:118576200-118591400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:118576200-118595400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:118576400-118591400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:118576600-118587600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:118576600-118590600	Strong transcription	Adipose Nuclei	Adipose
31	chr12:118576600-118590600	Strong transcription	Brain Germinal Matrix	brain
32	chr12:118576800-118585800	Strong transcription	Fetal Intestine Small	intestine
33	chr12:118576800-118587400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:118577200-118587800	Strong transcription	NHDF-Ad	bronchial
35	chr12:118577400-118586600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:118577400-118601800	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:118577600-118586200	Strong transcription	Ovary	ovary
38	chr12:118577600-118586600	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr12:118577600-118586800	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr12:118577600-118587800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:118577600-118590800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:118577600-118599000	Weak transcription	Psoas Muscle	Psoas
43	chr12:118578000-118590800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr12:118578200-118586800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr12:118578200-118588000	Strong transcription	Brain Anterior Caudate	brain
46	chr12:118578200-118588400	Weak transcription	K562	blood
47	chr12:118578200-118611600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:118578600-118603200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr12:118579600-118588400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:118580400-118590600	Strong transcription	Spleen	Spleen

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