Variant report

Variant	rs1194596
Chromosome Location	chr1:154238383-154238384
allele	A/G
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	chr1:154238154-154238432	K562	blood:	n/a	n/a
2	POLR2A	chr1:154238176-154239306	Hela-S3	cervix:	n/a	n/a
3	NFATC1	chr1:154237336-154239144	GM12878	blood:	n/a	chr1:154237361-154237375
4	POLR2A	chr1:154238108-154239236	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr1:154232935-154239560	K562	blood:	n/a	n/a
6	POLR2A	chr1:154238227-154238605	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:154238078-154238540	GM12892	blood:	n/a	n/a
8	NFATC1	chr1:154238038-154239025	GM12878	blood:	n/a	n/a
9	RUNX3	chr1:154237995-154238403	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154192034..154195055-chr1:154237858..154241372,4	MCF-7	breast:
2	chr1:154228115..154231882-chr1:154235436..154238955,4	MCF-7	breast:
3	chr1:154236442..154241812-chr1:154243586..154247600,7	MCF-7	breast:
4	chr1:154227049..154228742-chr1:154236510..154238440,2	MCF-7	breast:

Variant related genes	Relation type
UBAP2L	TF binding region
ENSG00000143612	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143575	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10158820	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1044013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10797047	0.88[ASN][1000 genomes]
rs10797061	0.80[GIH][hapmap]
rs11265238	0.91[JPT][hapmap]
rs11265251	0.82[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11265425	0.95[JPT][hapmap]
rs11586902	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11802893	0.86[JPT][hapmap]
rs1194580	0.80[GIH][hapmap]
rs1194593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194603	0.80[GIH][hapmap]
rs1194604	0.80[GIH][hapmap]
rs12023901	0.83[ASN][1000 genomes]
rs12025237	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12026177	0.91[JPT][hapmap]
rs12026615	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12027999	0.84[ASN][1000 genomes]
rs12028554	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12028949	0.91[JPT][hapmap]
rs12029331	0.86[ASN][1000 genomes]
rs12062977	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1212352	0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs12733060	0.84[ASN][1000 genomes]
rs12738393	0.84[ASN][1000 genomes]
rs12743874	0.80[ASN][1000 genomes]
rs12750321	0.80[ASN][1000 genomes]
rs16835846	0.87[JPT][hapmap]
rs16835852	0.87[JPT][hapmap]
rs1760802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1760803	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1986709	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2220390	0.80[GIH][hapmap]
rs2274993	0.81[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2282227	0.87[ASN][1000 genomes]
rs2340473	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2879788	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3762339	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3762340	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3790613	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3790614	0.84[ASN][1000 genomes]
rs3811453	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs3811455	0.91[JPT][hapmap]
rs3828077	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3935419	0.91[JPT][hapmap]
rs4240871	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4620534	0.91[JPT][hapmap]
rs6427509	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6657214	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6667222	0.87[ASW][hapmap];0.83[LWK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs6673752	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6719	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7517578	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7524346	0.83[ASN][1000 genomes]
rs9803857	0.86[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9803862	0.80[GIH][hapmap]
rs9804045	0.80[GIH][hapmap]
rs9943093	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1194596	C1orf43	cis	parietal	SCAN
rs1194596	HAX1	cis	lymphoblastoid	seeQTL
rs1194596	SPRR2D	cis	parietal	SCAN
rs1194596	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL
rs1194596	UBAP2L	cis	multi-tissue	Pritchard
rs1194596	HAX1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154195600-154244000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:154196200-154243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:154196400-154243800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:154196600-154243600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:154196800-154242600	Strong transcription	A549	lung
6	chr1:154197000-154242800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:154197400-154242800	Strong transcription	Brain Anterior Caudate	brain
14	chr1:154197600-154239200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:154197600-154239200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr1:154197600-154239400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:154197600-154239800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:154197600-154239800	Strong transcription	NHLF	lung
19	chr1:154197600-154242000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:154197600-154243000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:154197600-154243600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr1:154197600-154243600	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr1:154197600-154243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:154197600-154243600	Strong transcription	Thymus	Thymus
25	chr1:154197600-154243800	Strong transcription	Adipose Nuclei	Adipose
26	chr1:154197600-154244000	Strong transcription	Fetal Muscle Leg	muscle
27	chr1:154197800-154239600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:154197800-154242000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:154197800-154243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:154197800-154243600	Strong transcription	Placenta	Placenta
31	chr1:154197800-154243800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:154198000-154243000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:154198000-154243800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr1:154198200-154241000	Strong transcription	Dnd41	blood
35	chr1:154198400-154243000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:154199000-154243600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:154199400-154243600	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:154200000-154243800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:154205800-154239200	Strong transcription	NHDF-Ad	bronchial
40	chr1:154211000-154243800	Strong transcription	Fetal Intestine Large	intestine
41	chr1:154212000-154239600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:154212200-154239800	Strong transcription	Liver	Liver
43	chr1:154212800-154240200	Strong transcription	Left Ventricle	heart
44	chr1:154213000-154242800	Strong transcription	Colon Smooth Muscle	Colon
45	chr1:154213200-154239000	Strong transcription	HepG2	liver
46	chr1:154213600-154243800	Strong transcription	Brain Hippocampus Middle	brain
47	chr1:154214000-154239600	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr1:154214000-154239600	Strong transcription	HMEC	breast
49	chr1:154214000-154243600	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr1:154214000-154243800	Strong transcription	Stomach Smooth Muscle	stomach

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