Variant report

Variant	rs12138074
Chromosome Location	chr1:227970556-227970557
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	chr1:227963179..227967609-chr1:227968212..227971433,3	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10799447	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10799448	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10799449	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916205	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916207	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs12132275	0.87[ASN][1000 genomes]
rs17555357	0.88[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2236359	0.88[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2281708	0.98[ASN][1000 genomes]
rs2295994	0.81[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653872	0.91[ASN][1000 genomes]
rs6672002	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6683757	0.80[CEU][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6683869	0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6696944	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6697054	0.97[ASN][1000 genomes]
rs7526021	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
8	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
11	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12138074	SNAP47	cis	lymphoblastoid	seeQTL
rs12138074	C1orf142	Cis_1M	lymphoblastoid	RTeQTL
rs12138074	WDR26	cis	cerebellum	SCAN
rs12138074	HIST3H2A	cis	parietal	SCAN
rs12138074	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227950800-227974200	Weak transcription	Small Intestine	intestine
2	chr1:227951200-227974400	Weak transcription	Right Atrium	heart
3	chr1:227951800-227970600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:227954400-227974600	Weak transcription	HMEC	breast
5	chr1:227955600-227973200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:227955600-227974000	Weak transcription	Fetal Brain Male	brain
7	chr1:227955800-227972400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:227955800-227974800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:227955800-227975200	Weak transcription	Hela-S3	cervix
10	chr1:227956000-227974600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:227956600-227973000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:227957600-227972800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:227957800-227974600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:227958000-227975200	Weak transcription	A549	lung
15	chr1:227962000-227974200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:227962400-227973400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:227962400-227974200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:227962600-227973400	Weak transcription	Primary B cells from cord blood	blood
19	chr1:227962800-227974000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:227963800-227974000	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:227964000-227973800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:227964200-227973400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:227964200-227973600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:227964400-227972600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:227964400-227973200	Weak transcription	HepG2	liver
26	chr1:227964400-227973400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:227964400-227973800	Weak transcription	Fetal Heart	heart
28	chr1:227964400-227974000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:227964400-227975000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:227964600-227971400	Weak transcription	HUVEC	blood vessel
31	chr1:227964600-227971800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:227964600-227973400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:227964600-227973400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:227964600-227973400	Weak transcription	GM12878-XiMat	blood
35	chr1:227964600-227974000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:227965200-227973000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:227965200-227973600	Weak transcription	Left Ventricle	heart
38	chr1:227967000-227973600	Weak transcription	Osteobl	bone
39	chr1:227967400-227973800	Weak transcription	NHDF-Ad	bronchial
40	chr1:227967400-227974000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:227967800-227970600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:227967800-227974800	Weak transcription	NH-A	brain
43	chr1:227968000-227970600	Strong transcription	Fetal Muscle Leg	muscle
44	chr1:227968000-227974200	Weak transcription	HSMM	muscle
45	chr1:227968200-227970600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:227968200-227970600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:227968200-227971000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:227968200-227973400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:227968400-227973600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:227968600-227971400	Weak transcription	NHEK	skin

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