Variant report

Variant	rs9633354
Chromosome Location	chr1:197644773-197644774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197637854..197639785-chr1:197643428..197645113,2	K562	blood:
2	chr1:197644483..197647407-chr1:197649632..197652293,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10754228	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs10801620	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10922252	0.81[ASN][1000 genomes]
rs10922259	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10922260	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs10922266	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1135810	0.90[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs12042609	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs12066841	0.92[ASN][1000 genomes]
rs12081207	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs1998711	0.92[ASN][1000 genomes]
rs2111930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2111934	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4026508	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4026514	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs4274099	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4282851	0.95[ASN][1000 genomes]
rs4611052	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4915561	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs55995691	0.90[ASN][1000 genomes]
rs6428416	1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs6667560	0.82[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs6667685	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6675292	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs6688289	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516153	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7516334	0.89[ASN][1000 genomes]
rs7516481	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[ASN][1000 genomes]
rs7523627	0.91[ASN][1000 genomes]
rs7533766	0.94[ASN][1000 genomes]
rs7548454	0.95[ASN][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	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv437263	chr1:197599030-197722240	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv873077	chr1:197615391-197698103	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9633354	DENND1B	cis	parietal	SCAN
rs9633354	LHX2	trans	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197596600-197644800	Weak transcription	Ovary	ovary
2	chr1:197603200-197645000	Weak transcription	Esophagus	oesophagus
3	chr1:197611800-197644800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr1:197612800-197644800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:197612800-197645000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:197628800-197645000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:197629000-197645000	Weak transcription	Dnd41	blood
8	chr1:197629000-197645200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:197640800-197644800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:197640800-197644800	Weak transcription	Fetal Intestine Small	intestine
11	chr1:197640800-197647000	Weak transcription	Small Intestine	intestine
12	chr1:197640800-197657600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:197641800-197645000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:197642800-197645400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:197642800-197645800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:197642800-197646800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:197643200-197645600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr1:197643400-197645400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:197643600-197645000	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:197643600-197645000	Weak transcription	Pancreas	Pancrea
21	chr1:197643800-197646800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:197644000-197644800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:197644000-197645000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:197644000-197645000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:197644000-197656000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:197644200-197645600	Enhancers	Fetal Brain Female	brain
27	chr1:197644200-197645800	Enhancers	Fetal Brain Male	brain
28	chr1:197644400-197644800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:197644400-197644800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:197644400-197645000	Active TSS	Stomach Mucosa	stomach
31	chr1:197644400-197645200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:197644400-197645400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:197644400-197645600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:197644600-197644800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:197644600-197644800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:197644600-197644800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:197644600-197644800	Flanking Active TSS	Liver	Liver
38	chr1:197644600-197644800	Flanking Active TSS	Fetal Lung	lung
39	chr1:197644600-197644800	Flanking Active TSS	A549	lung
40	chr1:197644600-197645000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:197644600-197645000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:197644600-197645000	Active TSS	K562	blood
43	chr1:197644600-197645000	Active TSS	NHDF-Ad	bronchial
44	chr1:197644600-197645200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:197644600-197645200	Active TSS	Adipose Nuclei	Adipose
46	chr1:197644600-197645200	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr1:197644600-197645200	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr1:197644600-197645200	Active TSS	HMEC	breast
49	chr1:197644600-197645200	Active TSS	HUVEC	blood vessel
50	chr1:197644600-197645200	Active TSS	NHEK	skin

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