Variant report

Variant	rs2236359
Chromosome Location	chr1:227935444-227935445
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227934449-227938226	PBDE	blood:	n/a	n/a
2	MAZ	chr1:227935436-227935456	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
2	chr1:227921956..227924183-chr1:227932541..227935696,3	MCF-7	breast:

Variant related genes	Relation type
SNAP47	TF binding region
SNAP47-AS1	TF binding region
ENSG00000081692	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10799447	0.90[JPT][hapmap]
rs10799448	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10799449	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10916205	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916207	0.85[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12138074	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17555357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2281708	0.87[ASN][1000 genomes]
rs2295994	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3088389	0.84[YRI][hapmap]
rs6664307	0.89[YRI][hapmap]
rs6672002	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6683757	0.90[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6683869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6696944	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6697054	0.88[ASN][1000 genomes]
rs7526021	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS 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	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2236359	WDR26	cis	cerebellum	SCAN
rs2236359	SUSD4	cis	cerebellum	SCAN
rs2236359	C1orf142	Cis_1M	lymphoblastoid	RTeQTL
rs2236359	HIST3H2A	cis	parietal	SCAN
rs2236359	SNAP47	cis	multi-tissue	Pritchard
rs2236359	SNAP47	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227923800-227935600	Weak transcription	Aorta	Aorta
2	chr1:227924000-227935600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:227924000-227936400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:227924200-227935600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:227924200-227935600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:227924200-227935800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:227924200-227935800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:227924200-227935800	Weak transcription	A549	lung
9	chr1:227924200-227936000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:227924200-227936000	Weak transcription	Fetal Kidney	kidney
11	chr1:227924200-227940800	Weak transcription	HSMMtube	muscle
12	chr1:227924200-227941200	Weak transcription	HSMM	muscle
13	chr1:227924200-227941200	Weak transcription	NHDF-Ad	bronchial
14	chr1:227924200-227941600	Weak transcription	Osteobl	bone
15	chr1:227924200-227942000	Weak transcription	Hela-S3	cervix
16	chr1:227924200-227946800	Weak transcription	HUVEC	blood vessel
17	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:227924400-227935800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:227924400-227936200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:227924800-227935600	Weak transcription	Colonic Mucosa	Colon
21	chr1:227924800-227941400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:227925000-227935600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:227925000-227936000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:227925000-227941400	Weak transcription	Fetal Brain Male	brain
25	chr1:227925200-227935600	Weak transcription	HepG2	liver
26	chr1:227925200-227941200	Weak transcription	Psoas Muscle	Psoas
27	chr1:227925400-227935600	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:227925600-227935800	Weak transcription	GM12878-XiMat	blood
29	chr1:227925600-227941800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:227928600-227941200	Weak transcription	Small Intestine	intestine
31	chr1:227929200-227935800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:227930200-227945600	Weak transcription	NH-A	brain
33	chr1:227930400-227939400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:227930600-227935800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:227931800-227935600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:227931800-227938400	Weak transcription	NHEK	skin
37	chr1:227932800-227935600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:227932800-227941400	Weak transcription	Stomach Mucosa	stomach
39	chr1:227932800-227947200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:227933000-227935600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:227933000-227939400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:227933000-227946400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:227933200-227935600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:227933200-227935800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:227933400-227935600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:227933400-227935600	Enhancers	Ovary	ovary
47	chr1:227933400-227936200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:227933600-227935600	Weak transcription	Fetal Thymus	thymus
49	chr1:227933800-227939000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:227934000-227938600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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