Variant report

Variant	rs7988945
Chromosome Location	chr13:51496320-51496321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51482808..51485388-chr13:51495589..51498006,3	K562	blood:
2	chr13:51495576..51498047-chr13:51500874..51502897,3	K562	blood:

Variant related genes	Relation type
ENSG00000233672	Chromatin interaction
ENSG00000136104	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17074987	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038718	0.85[YRI][hapmap]
rs2274069	0.91[ASN][1000 genomes]
rs4941677	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941678	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4942943	0.92[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59310144	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561599	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs6561601	0.84[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6561602	0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs6561603	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs730076	0.85[YRI][hapmap]
rs7316955	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7317618	0.91[CHD][hapmap]
rs7321027	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7324232	0.84[ASW][hapmap];0.86[CHD][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[AFR][1000 genomes]
rs7329171	0.93[CHD][hapmap];0.85[YRI][hapmap]
rs9316512	0.85[YRI][hapmap]
rs9535523	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535526	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535531	0.82[GIH][hapmap]
rs9535534	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900077	chr13:51446114-51514831	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7988945	RNASEH2B	cis	Artery Tibial	GTEx
rs7988945	RNASEH2B	cis	parietal	SCAN
rs7988945	RNASEH2B	cis	temporal cortex	BrainEAC
rs7988945	RNASEH2B	cis	occipital cortex	BrainEAC
rs7988945	RNASEH2B	cis	frontal cortex	BrainEAC
rs7988945	RNASEH2B	cis	Esophagus Muscularis	GTEx
rs7988945	RNASEH2B	cis	intralobular white matter	BrainEAC
rs7988945	RNASEH2B	cis	Thyroid	GTEx
rs7988945	RNASEH2B	cis	cerebellar cortex	BrainEAC
rs7988945	RNASEH2B	cis	cerebellum	SCAN
rs7988945	RNASEH2B	cis	Muscle Skeletal	GTEx
rs7988945	RNASEH2B	cis	brain	BrainEAC
rs7988945	RNASEH2B	cis	thalamus	BrainEAC

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51485400-51504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:51486600-51528400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:51487000-51498400	Weak transcription	Fetal Stomach	stomach
4	chr13:51489600-51496400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr13:51489600-51496400	Weak transcription	Fetal Kidney	kidney
6	chr13:51489600-51508200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr13:51490000-51496400	Weak transcription	Aorta	Aorta
8	chr13:51491400-51496400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr13:51491400-51496600	Weak transcription	Fetal Intestine Large	intestine
10	chr13:51491400-51497000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr13:51491600-51551000	Weak transcription	Small Intestine	intestine
12	chr13:51491800-51499000	ZNF genes & repeats	Dnd41	blood
13	chr13:51492200-51496400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr13:51493000-51496400	Weak transcription	Lung	lung
15	chr13:51493600-51496400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr13:51493600-51496400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr13:51493600-51496400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr13:51493800-51504800	Weak transcription	Right Ventricle	heart
19	chr13:51494000-51496800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr13:51494000-51502400	Weak transcription	Fetal Heart	heart
21	chr13:51494400-51497200	Weak transcription	Brain Anterior Caudate	brain
22	chr13:51494800-51500400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr13:51495000-51500400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr13:51495200-51497200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
25	chr13:51495200-51498800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr13:51495200-51500200	ZNF genes & repeats	Primary B cells from cord blood	blood
27	chr13:51495200-51500400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr13:51495400-51497000	ZNF genes & repeats	Fetal Muscle Leg	muscle
29	chr13:51495400-51497000	ZNF genes & repeats	Thymus	Thymus
30	chr13:51495400-51497600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr13:51495400-51498800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr13:51495600-51496600	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr13:51495600-51497000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
34	chr13:51495600-51500400	ZNF genes & repeats	Primary T cells from cord blood	blood
35	chr13:51495800-51497000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
36	chr13:51495800-51497000	ZNF genes & repeats	Fetal Brain Female	brain
37	chr13:51495800-51497000	ZNF genes & repeats	GM12878-XiMat	blood
38	chr13:51495800-51499800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr13:51496000-51496400	ZNF genes & repeats	Liver	Liver
40	chr13:51496000-51496600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
41	chr13:51496000-51496600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr13:51496000-51496600	ZNF genes & repeats	Left Ventricle	heart
43	chr13:51496000-51496800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
44	chr13:51496000-51496800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr13:51496000-51496800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
46	chr13:51496000-51496800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
47	chr13:51496000-51496800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr13:51496000-51496800	ZNF genes & repeats	Fetal Thymus	thymus
49	chr13:51496000-51496800	ZNF genes & repeats	A549	lung
50	chr13:51496000-51496800	ZNF genes & repeats	HSMM	muscle

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