Variant report

Variant	rs4893824
Chromosome Location	chr2:178298104-178298105
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	JUND	chr2:178298044-178298646	SK-N-SH	brain:	n/a	chr2:178298288-178298299
2	CBX3	chr2:178298029-178298766	K562	blood:	n/a	n/a
3	TRIM28	chr2:178298042-178298569	K562	blood:	n/a	n/a
4	KAP1	chr2:178297837-178298841	K562	blood:	n/a	n/a
5	SETDB1	chr2:178297543-178298980	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178127146..178129590-chr2:178297800..178300708,2	K562	blood:

Variant related genes	Relation type
AGPS	TF binding region
ENSG00000222043	Chromatin interaction
ENSG00000116044	Chromatin interaction

Extended variants
information (count: 189 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:187)

rs_ID	r²[population]
rs10165785	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170546	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10170667	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10176632	0.80[ASN][1000 genomes]
rs10176724	0.83[AFR][1000 genomes]
rs10180514	0.82[AFR][1000 genomes]
rs10184488	0.86[AFR][1000 genomes]
rs10190306	0.86[AFR][1000 genomes]
rs10194452	0.86[AFR][1000 genomes]
rs10194648	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10208150	0.80[ASN][1000 genomes]
rs10497502	0.85[ASN][1000 genomes]
rs10497503	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10497504	0.81[AFR][1000 genomes]
rs10497508	0.88[ASN][1000 genomes]
rs10497509	0.89[AFR][1000 genomes]
rs10754987	0.86[AFR][1000 genomes]
rs10754988	0.89[AFR][1000 genomes]
rs10803909	0.94[ASN][1000 genomes]
rs10803911	0.86[AFR][1000 genomes]
rs10803912	0.81[AFR][1000 genomes]
rs10930788	0.89[AFR][1000 genomes]
rs10930790	0.89[AFR][1000 genomes]
rs10930791	0.89[AFR][1000 genomes]
rs10930792	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10930793	0.86[AFR][1000 genomes]
rs11891003	0.86[AFR][1000 genomes]
rs11893448	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12104588	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12469386	0.93[ASN][1000 genomes]
rs12478545	0.82[AFR][1000 genomes]
rs12612957	0.84[AFR][1000 genomes]
rs12616443	0.96[ASN][1000 genomes]
rs12618139	0.86[ASN][1000 genomes]
rs12621156	0.89[AFR][1000 genomes]
rs12693120	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12693121	0.82[AFR][1000 genomes]
rs12990729	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12996447	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13000048	0.93[ASN][1000 genomes]
rs13004955	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13027959	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1345138	0.81[AFR][1000 genomes]
rs1348848	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1348849	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1374437	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1374438	0.83[AFR][1000 genomes]
rs1446838	0.82[AFR][1000 genomes]
rs1453370	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1453371	0.80[ASN][1000 genomes]
rs1530965	0.86[AFR][1000 genomes]
rs16865203	0.88[ASN][1000 genomes]
rs16865216	0.88[ASN][1000 genomes]
rs16865229	0.88[ASN][1000 genomes]
rs16865291	0.86[ASN][1000 genomes]
rs1838890	0.81[AFR][1000 genomes]
rs1867905	0.81[AFR][1000 genomes]
rs1901823	0.89[AFR][1000 genomes]
rs1901824	0.86[ASN][1000 genomes]
rs1901825	0.86[ASN][1000 genomes]
rs1901826	0.80[ASN][1000 genomes]
rs1901829	0.88[ASN][1000 genomes]
rs1979058	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979059	0.86[AFR][1000 genomes]
rs2060929	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2084233	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2084966	0.89[AFR][1000 genomes]
rs2100395	0.82[AFR][1000 genomes]
rs2121430	0.96[ASN][1000 genomes]
rs2123643	0.89[AFR][1000 genomes]
rs2141157	0.83[AFR][1000 genomes]
rs2166556	0.83[AFR][1000 genomes]
rs2166557	0.82[AFR][1000 genomes]
rs2166558	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2167902	0.89[AFR][1000 genomes]
rs2197611	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2218575	0.81[AFR][1000 genomes]
rs2293475	0.81[AFR][1000 genomes]
rs2364845	0.86[ASN][1000 genomes]
rs2364852	0.81[AFR][1000 genomes]
rs2364853	0.84[ASN][1000 genomes]
rs2364854	0.93[ASN][1000 genomes]
rs3754989	0.89[AFR][1000 genomes]
rs3769995	0.86[ASN][1000 genomes]
rs3769996	0.86[ASN][1000 genomes]
rs3769997	0.86[ASN][1000 genomes]
rs3770002	0.87[ASN][1000 genomes]
rs3813259	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813260	0.87[AFR][1000 genomes]
rs3902850	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4243388	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4243389	0.83[AFR][1000 genomes]
rs4308151	0.89[AFR][1000 genomes]
rs4335983	0.86[AFR][1000 genomes]
rs4341974	0.94[ASN][1000 genomes]
rs4350784	0.89[AFR][1000 genomes]
rs4402804	0.85[AFR][1000 genomes]
rs4585065	0.86[AFR][1000 genomes]
rs4893821	0.86[ASN][1000 genomes]
rs4893822	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4893823	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4893825	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893826	0.89[AFR][1000 genomes]
rs4893827	0.89[AFR][1000 genomes]
rs4893829	0.81[AFR][1000 genomes]
rs4893931	0.82[ASN][1000 genomes]
rs4893932	0.86[ASN][1000 genomes]
rs4893934	0.86[ASN][1000 genomes]
rs4893935	0.84[ASN][1000 genomes]
rs4893936	0.87[ASN][1000 genomes]
rs4893938	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4893940	0.89[AFR][1000 genomes]
rs4893941	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4893942	0.87[AFR][1000 genomes]
rs4893943	0.89[AFR][1000 genomes]
rs4893944	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4893945	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4893946	0.94[ASN][1000 genomes]
rs4893950	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4893951	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4893954	0.93[ASN][1000 genomes]
rs4893955	0.82[AFR][1000 genomes]
rs4893956	0.83[AFR][1000 genomes]
rs4893957	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4893959	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4893961	0.84[ASN][1000 genomes]
rs56942680	0.84[ASN][1000 genomes]
rs57273542	0.87[ASN][1000 genomes]
rs57295810	0.86[ASN][1000 genomes]
rs57527255	0.87[ASN][1000 genomes]
rs57541536	0.87[ASN][1000 genomes]
rs57733896	0.85[ASN][1000 genomes]
rs57890299	0.81[AFR][1000 genomes]
rs57948641	0.87[ASN][1000 genomes]
rs58297927	0.87[ASN][1000 genomes]
rs58483300	0.84[ASN][1000 genomes]
rs59111239	0.88[ASN][1000 genomes]
rs59421055	0.83[ASN][1000 genomes]
rs59504156	0.86[ASN][1000 genomes]
rs60642012	0.83[ASN][1000 genomes]
rs60670838	0.88[ASN][1000 genomes]
rs60733259	0.84[ASN][1000 genomes]
rs6433664	0.89[AFR][1000 genomes]
rs6433670	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433673	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6433674	0.82[AFR][1000 genomes]
rs6433675	0.82[AFR][1000 genomes]
rs6433676	0.82[AFR][1000 genomes]
rs6433677	0.82[AFR][1000 genomes]
rs6710109	0.83[AFR][1000 genomes]
rs6710575	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6715365	0.82[AFR][1000 genomes]
rs6717457	0.89[AFR][1000 genomes]
rs6719114	0.86[AFR][1000 genomes]
rs6721168	0.83[AFR][1000 genomes]
rs6723014	0.81[AFR][1000 genomes]
rs6725096	0.84[AFR][1000 genomes]
rs6732250	0.89[AFR][1000 genomes]
rs6741974	0.89[AFR][1000 genomes]
rs6742951	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6744488	0.82[AFR][1000 genomes]
rs6759567	0.85[AFR][1000 genomes]
rs7565022	0.96[ASN][1000 genomes]
rs7568452	0.86[AFR][1000 genomes]
rs7570297	0.89[AFR][1000 genomes]
rs7573763	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7582179	0.81[AFR][1000 genomes]
rs7585952	0.89[AFR][1000 genomes]
rs7586051	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587604	0.96[ASN][1000 genomes]
rs7588049	0.81[AFR][1000 genomes]
rs7589927	0.84[AFR][1000 genomes]
rs7591807	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7594073	0.87[AFR][1000 genomes]
rs7601132	0.86[AFR][1000 genomes]
rs7604668	0.82[AFR][1000 genomes]
rs7604673	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7606235	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7607073	0.83[AFR][1000 genomes]
rs7607450	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7608135	0.86[AFR][1000 genomes]
rs8941	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs935426	0.81[AFR][1000 genomes]
rs952746	0.96[ASN][1000 genomes]
rs9679607	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9789580	0.86[AFR][1000 genomes]
rs9789582	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4893824	DKFZp451M2119	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178287200-178300000	Weak transcription	Hela-S3	cervix
2	chr2:178287200-178310600	Weak transcription	Stomach Mucosa	stomach
3	chr2:178287600-178314200	Weak transcription	Gastric	stomach
4	chr2:178289400-178299400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:178291000-178299400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:178291600-178299200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
7	chr2:178291800-178299000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr2:178291800-178299200	ZNF genes & repeats	Primary B cells from cord blood	blood
9	chr2:178292800-178299400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
10	chr2:178293600-178298800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr2:178293800-178298800	ZNF genes & repeats	Dnd41	blood
12	chr2:178293800-178299000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:178294000-178299400	ZNF genes & repeats	Fetal Muscle Leg	muscle
14	chr2:178294200-178298400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr2:178294200-178299400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:178294400-178298800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
17	chr2:178295400-178329800	Weak transcription	Pancreas	Pancrea
18	chr2:178295400-178330000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:178295400-178330200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:178295600-178306200	Weak transcription	Osteobl	bone
21	chr2:178296000-178298400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
22	chr2:178296000-178298800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:178296000-178299200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
24	chr2:178296200-178298800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr2:178296200-178299200	ZNF genes & repeats	Primary T cells from cord blood	blood
26	chr2:178296400-178298800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:178296400-178299200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:178296400-178397000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:178296600-178298800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:178296600-178299000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
31	chr2:178296600-178319800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:178296800-178306800	Weak transcription	Placenta	Placenta
33	chr2:178296800-178310000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:178297000-178298400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:178297000-178298400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
36	chr2:178297000-178299000	ZNF genes & repeats	Liver	Liver
37	chr2:178297000-178299200	ZNF genes & repeats	GM12878-XiMat	blood
38	chr2:178297000-178299200	ZNF genes & repeats	K562	blood
39	chr2:178297000-178306000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:178297000-178313400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:178297200-178298400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
42	chr2:178297200-178298800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:178297200-178315400	Strong transcription	HepG2	liver
44	chr2:178297400-178298600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:178297400-178298800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr2:178297400-178298800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:178297400-178299000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:178297400-178299000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
49	chr2:178297400-178299000	ZNF genes & repeats	Fetal Lung	lung
50	chr2:178297400-178299000	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links