Variant report

Variant	rs1344272
Chromosome Location	chr2:173353318-173353319
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	FOXA1	chr2:173353116-173353592	HepG2	liver:	n/a	n/a
2	ARID3A	chr2:173353268-173353556	HepG2	liver:	n/a	n/a
3	TEAD4	chr2:173353153-173353654	HepG2	liver:	n/a	chr2:173353455-173353464
4	HNF4A	chr2:173353257-173353614	HepG2	liver:	n/a	n/a
5	MXI1	chr2:173353253-173353633	HepG2	liver:	n/a	chr2:173353584-173353593 chr2:173353513-173353522
6	FOXA2	chr2:173353235-173353553	HepG2	liver:	n/a	n/a
7	SMC3	chr2:173353317-173353758	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:173352292..173355193-chr2:173355588..173357472,2	K562	blood:
2	chr2:173351396..173353492-chr2:173418976..173421854,2	K562	blood:
3	chr2:173352359..173353981-chr2:173354286..173356904,2	MCF-7	breast:

Variant related genes	Relation type
ITGA6	TF binding region
ENSG00000225205	Chromatin interaction
ENSG00000091409	Chromatin interaction
ENSG00000152256	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10497383	0.93[CEU][hapmap]
rs10497384	0.93[CEU][hapmap]
rs1076595	0.82[JPT][hapmap]
rs10930558	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs11883720	0.93[CEU][hapmap]
rs11896937	0.93[CEU][hapmap]
rs11897024	0.93[CEU][hapmap]
rs12465295	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12465442	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12467358	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12469958	0.82[ASN][1000 genomes]
rs12473999	0.81[ASN][1000 genomes]
rs12474168	0.82[ASN][1000 genomes]
rs12474995	0.82[ASN][1000 genomes]
rs12475916	0.81[ASN][1000 genomes]
rs12477247	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12477594	0.82[JPT][hapmap]
rs12478465	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12619242	0.82[ASN][1000 genomes]
rs12622687	0.82[ASN][1000 genomes]
rs13383151	0.82[ASN][1000 genomes]
rs13402061	0.82[ASN][1000 genomes]
rs1574247	0.82[ASN][1000 genomes]
rs1574258	0.93[CEU][hapmap]
rs16860543	0.84[ASN][1000 genomes]
rs17286988	0.93[CEU][hapmap]
rs17676773	0.93[CEU][hapmap]
rs17677404	0.93[CEU][hapmap]
rs17727678	0.93[CEU][hapmap]
rs17727732	0.93[CEU][hapmap]
rs17739735	0.93[CEU][hapmap]
rs17739946	0.93[CEU][hapmap]
rs2178474	0.82[ASN][1000 genomes]
rs2178475	0.93[CEU][hapmap]
rs2272498	0.93[CEU][hapmap]
rs2293646	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2293649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2357415	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs34094408	0.82[ASN][1000 genomes]
rs3792255	0.93[CEU][hapmap]
rs3792256	0.93[CEU][hapmap]
rs3792257	0.80[ASN][1000 genomes]
rs3792260	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs3828342	0.93[CEU][hapmap]
rs4308101	0.82[ASN][1000 genomes]
rs4619573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972510	0.86[CEU][hapmap]
rs4972511	0.93[CEU][hapmap]
rs4972832	0.93[CEU][hapmap]
rs4972839	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56084828	0.85[ASN][1000 genomes]
rs57957394	0.82[ASN][1000 genomes]
rs58016698	0.82[ASN][1000 genomes]
rs58044442	0.82[ASN][1000 genomes]
rs59020762	0.82[ASN][1000 genomes]
rs59524026	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59610589	0.82[ASN][1000 genomes]
rs60275829	0.84[ASN][1000 genomes]
rs60442917	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60446415	0.82[ASN][1000 genomes]
rs6433359	0.93[CEU][hapmap]
rs6433360	0.93[CEU][hapmap]
rs6715294	0.93[CEU][hapmap]
rs6718477	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6728419	0.93[CEU][hapmap]
rs6731691	0.93[CEU][hapmap]
rs6755100	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6755605	0.93[CEU][hapmap]
rs72894386	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7564591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7564654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7565216	0.82[ASN][1000 genomes]
rs7582972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7591883	0.82[ASN][1000 genomes]
rs7609465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173321400-173356000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173327800-173370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:173328800-173353400	Weak transcription	Right Ventricle	heart
4	chr2:173329800-173371200	Weak transcription	Hela-S3	cervix
5	chr2:173330400-173360400	Weak transcription	Small Intestine	intestine
6	chr2:173330600-173353400	Weak transcription	Fetal Stomach	stomach
7	chr2:173330600-173371400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:173330600-173372200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:173330600-173373200	Strong transcription	NHEK	skin
10	chr2:173330600-173373400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:173330600-173373400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:173330600-173373600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:173330600-173374200	Weak transcription	Stomach Mucosa	stomach
14	chr2:173331000-173370000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr2:173331000-173373200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:173331000-173373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:173331000-173373800	Strong transcription	HMEC	breast
18	chr2:173331200-173372000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:173331400-173370200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:173335400-173354000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:173337800-173360200	Strong transcription	Fetal Thymus	thymus
22	chr2:173342600-173353600	Weak transcription	A549	lung
23	chr2:173343000-173360200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:173344000-173356000	Weak transcription	Fetal Kidney	kidney
25	chr2:173345600-173353600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:173345800-173359800	Weak transcription	Placenta	Placenta
27	chr2:173345800-173360800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr2:173346000-173354200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:173346000-173360800	Strong transcription	HSMM	muscle
30	chr2:173346000-173370200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:173346000-173370200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:173346000-173370600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:173346400-173354000	Strong transcription	Fetal Intestine Small	intestine
34	chr2:173346400-173356000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:173346400-173371400	Weak transcription	NHLF	lung
36	chr2:173346600-173353400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:173346600-173356000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:173346600-173356000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:173346600-173357600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:173346800-173356000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:173347000-173367200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:173347200-173353400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:173347400-173368600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:173347800-173371600	Weak transcription	Fetal Brain Male	brain
45	chr2:173347800-173376200	Weak transcription	Fetal Heart	heart
46	chr2:173349200-173356800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr2:173349200-173357400	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:173349200-173358000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:173349400-173360200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:173349400-173360200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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