Variant report

Variant	rs56139516
Chromosome Location	chr1:149861829-149861830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:149861422-149861853	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:149854930-149863498	H1-hESC	embryonic stem cell:	n/a	n/a
3	HEY1	chr1:149855072-149862207	K562	blood:	n/a	n/a
4	POLR2A	chr1:149852655-149863016	K562	blood:	n/a	n/a
5	RFX5	chr1:149861791-149861912	K562	blood:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:149813928..149823076-chr1:149854513..149862208,33	K562	blood:
2	chr1:149859746..149861842-chr1:150028326..150031345,3	K562	blood:
3	chr1:149859746..149862142-chr1:150028326..150031401,5	K562	blood:
4	chr1:149854948..149862391-chr1:150036900..150043965,32	MCF-7	breast:
5	chr1:149857288..149861878-chr1:149980292..149985449,12	MCF-7	breast:
6	chr1:149855502..149862139-chr17:57919672..57925878,9	MCF-7	breast:
7	chr1:149855827..149861924-chr1:150032527..150042362,32	MCF-7	breast:
8	chr1:149854540..149863300-chr1:149979575..149985253,19	K562	blood:
9	chr1:149855536..149863300-chr1:149977462..149985642,29	K562	blood:
10	chr1:149780176..149786781-chr1:149856138..149862217,21	MCF-7	breast:
11	chr1:149860175..149862937-chr1:149996186..149999039,2	K562	blood:
12	chr1:149813697..149823354-chr1:149851773..149862006,115	MCF-7	breast:
13	chr1:149222054..149225122-chr1:149860268..149862340,3	MCF-7	breast:
14	chr1:149860773..149863100-chr1:149956381..149958493,2	K562	blood:
15	chr1:149813771..149823366-chr1:149853740..149862208,36	K562	blood:
16	chr1:149858428..149861867-chr1:150121197..150123185,3	K562	blood:
17	chr1:149854077..149861961-chr1:150131511..150145996,30	MCF-7	breast:
18	chr1:149860621..149862782-chr1:150182619..150184194,2	K562	blood:
19	chr1:149859688..149862015-chr20:52420095..52422543,2	MCF-7	breast:
20	chr1:149859690..149862582-chr1:149963642..149966186,2	K562	blood:
21	chr1:149860225..149861979-chr1:149968434..149970497,2	K562	blood:
22	chr1:149854392..149861957-chr1:150131544..150142194,21	K562	blood:
23	chr1:149855739..149863622-chr1:150034266..150042059,13	K562	blood:
24	chr1:149860176..149861953-chr1:149974831..149977107,2	K562	blood:

No data

Variant related genes	Relation type
HIST2H2BE	TF binding region
HIST2H2AB	TF binding region
ENSG00000242663	Chromatin interaction
ENSG00000220323	Chromatin interaction
ENSG00000183558	Chromatin interaction
ENSG00000183598	Chromatin interaction
ENSG00000203812	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000163113	Chromatin interaction
ENSG00000203814	Chromatin interaction
ENSG00000203819	Chromatin interaction
ENSG00000272993	Chromatin interaction
ENSG00000136631	Chromatin interaction
ENSG00000261716	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000266187	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1044808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1046332	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10494261	0.84[EUR][1000 genomes]
rs10494363	0.84[EUR][1000 genomes]
rs11205307	0.84[EUR][1000 genomes]
rs11205308	0.84[EUR][1000 genomes]
rs11577346	1.00[AFR][1000 genomes]
rs11584354	1.00[AFR][1000 genomes]
rs12062387	1.00[EUR][1000 genomes]
rs12077623	0.84[EUR][1000 genomes]
rs12078573	0.87[EUR][1000 genomes]
rs12081082	0.84[EUR][1000 genomes]
rs1349532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1376675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1376676	1.00[EUR][1000 genomes]
rs1451641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs15931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16835135	0.96[EUR][1000 genomes]
rs16836630	0.89[EUR][1000 genomes]
rs17643644	0.87[EUR][1000 genomes]
rs1804775	0.87[EUR][1000 genomes]
rs2044891	0.84[EUR][1000 genomes]
rs2198194	0.84[EUR][1000 genomes]
rs28560140	1.00[AFR][1000 genomes]
rs35230744	0.84[EUR][1000 genomes]
rs41264630	0.90[EUR][1000 genomes]
rs41265185	0.84[EUR][1000 genomes]
rs41302101	0.84[EUR][1000 genomes]
rs45548131	0.89[EUR][1000 genomes]
rs55633017	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55664407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55705001	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55840680	1.00[AFR][1000 genomes]
rs55885412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56119131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56212907	1.00[AFR][1000 genomes]
rs56229803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56265028	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs61355654	1.00[EUR][1000 genomes]
rs6587680	0.80[EUR][1000 genomes]
rs68002561	0.86[EUR][1000 genomes]
rs68144650	0.89[EUR][1000 genomes]
rs72692803	0.90[EUR][1000 genomes]
rs72692804	0.89[EUR][1000 genomes]
rs72692805	0.89[EUR][1000 genomes]
rs72692807	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72692808	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72692810	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72692811	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72692812	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72692813	0.87[EUR][1000 genomes]
rs72692814	0.87[EUR][1000 genomes]
rs72692816	0.87[EUR][1000 genomes]
rs72692818	0.87[EUR][1000 genomes]
rs72692819	0.87[EUR][1000 genomes]
rs72692873	1.00[AFR][1000 genomes]
rs72692886	1.00[AFR][1000 genomes]
rs72692893	1.00[AFR][1000 genomes]
rs72692898	1.00[AFR][1000 genomes]
rs72692899	1.00[AFR][1000 genomes]
rs72692900	1.00[AFR][1000 genomes]
rs72694914	1.00[AFR][1000 genomes]
rs72694915	1.00[AFR][1000 genomes]
rs72694923	1.00[AFR][1000 genomes]
rs72694926	1.00[AFR][1000 genomes]
rs72694928	1.00[AFR][1000 genomes]
rs72694933	1.00[AFR][1000 genomes]
rs72694936	1.00[AFR][1000 genomes]
rs72708145	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72708148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72708149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72708150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72708151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72708152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72708153	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72708157	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72708158	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72708162	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73008195	0.84[EUR][1000 genomes]
rs7524797	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432820	chr1:148921404-149920927	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	784 gene(s)	inside rSNPs	diseases
2	nsv831525	chr1:149701537-149878033	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
3	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149860800-149862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr1:149860800-149862800	Weak transcription	GM12878-XiMat	blood
3	chr1:149860800-149870600	Weak transcription	HepG2	liver
4	chr1:149860800-149871200	Weak transcription	Right Atrium	heart
5	chr1:149861000-149862800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:149861000-149871000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:149861400-149862000	Weak transcription	Placenta	Placenta
8	chr1:149861400-149862000	Enhancers	K562	blood
9	chr1:149861400-149862800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:149861400-149870800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links