Variant report

Variant	rs2232819
Chromosome Location	chr1:171755182-171755183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171712949..171715185-chr1:171753608..171756289,2	K562	blood:
2	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
3	chr1:171754075..171756411-chr1:171764040..171766145,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1045456	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489252	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913683	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913684	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091786	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565176	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12567851	0.88[EUR][1000 genomes]
rs12730717	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742601	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12750330	0.88[EUR][1000 genomes]
rs12753043	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17596025	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17596081	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17649609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17650310	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650340	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657363	0.91[EUR][1000 genomes]
rs1801898	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2143369	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2181216	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2223602	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2232807	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232813	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232824	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232825	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294718	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs236894	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs236897	0.87[EUR][1000 genomes]
rs236898	0.87[EUR][1000 genomes]
rs236899	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs236900	0.86[EUR][1000 genomes]
rs236907	1.00[CEU][hapmap]
rs34320898	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34627492	0.89[EUR][1000 genomes]
rs35249022	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35400839	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35631282	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35674909	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35882887	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35930163	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36080557	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3891278	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732843	0.91[EUR][1000 genomes]
rs56365362	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56377810	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807979	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6656852	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674364	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6675708	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6681322	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6687624	0.90[JPT][hapmap]
rs6689125	0.95[EUR][1000 genomes]
rs6695933	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7522582	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7536142	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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 target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv518222	chr1:171753039-171763549	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2232819	PIGC	cis	parietal	SCAN
rs2232819	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs2232819	RHOA	trans	parietal	SCAN
rs2232819	DUSP27	cis	parietal	SCAN
rs2232819	VAMP4	cis	cerebellum	SCAN
rs2232819	MAEL	cis	parietal	SCAN
rs2232819	METTL13	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:171752200-171759200	Weak transcription	Fetal Heart	heart
4	chr1:171752200-171762200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:171752200-171766600	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:171752200-171767400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:171752200-171768200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:171752400-171755400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:171752400-171755400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:171752400-171755400	Genic enhancers	K562	blood
11	chr1:171752400-171755600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:171752400-171766600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:171752400-171767200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:171752600-171755200	Genic enhancers	Stomach Smooth Muscle	stomach
15	chr1:171752600-171755600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
16	chr1:171752600-171756400	Strong transcription	NHEK	skin
17	chr1:171752600-171760000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:171752600-171767000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:171752600-171767000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:171752600-171767400	Strong transcription	Primary B cells from cord blood	blood
21	chr1:171752600-171767400	Strong transcription	A549	lung
22	chr1:171752600-171767800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:171752600-171767800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:171752800-171755400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:171752800-171755400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:171752800-171755400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:171752800-171755400	Genic enhancers	Lung	lung
28	chr1:171752800-171755600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:171752800-171755800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:171752800-171756000	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr1:171752800-171756000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:171752800-171757200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:171752800-171757800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:171752800-171761800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:171752800-171762600	Strong transcription	Fetal Stomach	stomach
36	chr1:171752800-171765800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:171752800-171766600	Strong transcription	Placenta	Placenta
38	chr1:171752800-171767200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr1:171752800-171770200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr1:171753000-171755400	Genic enhancers	Spleen	Spleen
41	chr1:171753000-171755600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr1:171753000-171756000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:171753000-171757800	Strong transcription	Brain Cingulate Gyrus	brain
44	chr1:171753000-171762000	Strong transcription	Colonic Mucosa	Colon
45	chr1:171753000-171763400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:171753000-171766200	Strong transcription	Brain Substantia Nigra	brain
47	chr1:171753000-171766800	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr1:171753000-171766800	Strong transcription	Brain Hippocampus Middle	brain
49	chr1:171753000-171767200	Strong transcription	Fetal Lung	lung
50	chr1:171753000-171767600	Strong transcription	Fetal Intestine Large	intestine

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