Variant report

Variant	rs772926
Chromosome Location	chr12:56440248-56440249
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:77)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:77 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56440010-56440430	Raji	blood:	n/a	n/a
2	POLR2A	chr12:56438456-56440437	K562	blood:	n/a	n/a
3	MTA3	chr12:56438824-56440626	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:56440136-56440479	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:56440154-56440414	A549	lung:	n/a	n/a
6	POLR2A	chr12:56438459-56440686	GM12891	blood:	n/a	n/a
7	POLR2A	chr12:56438442-56440629	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:56437986-56441151	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:56438153-56441424	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:56439927-56440280	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr12:56438344-56440599	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr12:56440187-56440340	A549	lung:	n/a	n/a
13	POLR2A	chr12:56438494-56440643	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr12:56440153-56440468	A549	lung:	n/a	n/a
15	POLR2A	chr12:56438473-56440539	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr12:56438226-56441381	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr12:56439891-56440617	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:56439931-56441193	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr12:56440074-56440539	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr12:56439932-56440588	K562	blood:	n/a	n/a
21	POLR2A	chr12:56438236-56441303	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr12:56438454-56440739	U87	brain:	n/a	n/a
23	POLR2A	chr12:56439878-56440785	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:56439927-56440513	HCT-116	colon:	n/a	n/a
25	POLR2A	chr12:56440010-56440774	HL-60	blood:	n/a	n/a
26	POLR2A	chr12:56439949-56440781	HL-60	blood:	n/a	n/a
27	POLR2A	chr12:56438852-56441257	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr12:56438745-56440930	HepG2	liver:	n/a	n/a
29	POLR2A	chr12:56438157-56441263	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:56438341-56440799	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr12:56438339-56441188	GM12892	blood:	n/a	n/a
32	POLR2A	chr12:56438416-56440547	K562	blood:	n/a	n/a
33	POLR2A	chr12:56439941-56440351	IMR90	lung:	n/a	n/a
34	POLR2A	chr12:56438454-56441401	U87	brain:	n/a	n/a
35	POLR2A	chr12:56439926-56440711	U87	brain:	n/a	n/a
36	POLR2A	chr12:56439892-56440686	Hela-S3	cervix:	n/a	n/a
37	PML	chr12:56438570-56441338	GM12878	blood:	n/a	n/a
38	NFATC1	chr12:56440097-56440473	GM12878	blood:	n/a	n/a
39	POLR2A	chr12:56440015-56440546	HepG2	liver:	n/a	n/a
40	POLR2A	chr12:56440214-56440347	MCF-7	breast:	n/a	n/a
41	POLR2A	chr12:56438425-56440614	HCT-116	colon:	n/a	n/a
42	POLR2A	chr12:56438577-56441166	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr12:56439916-56440552	ProgFib	skin:	n/a	n/a
44	POLR2A	chr12:56440129-56440352	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr12:56438477-56440727	SK-N-SH	brain:	n/a	n/a
46	STAT5A	chr12:56440206-56440535	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:56438817-56441273	ECC-1	luminal epithelium:	n/a	n/a
48	MTA3	chr12:56439921-56440331	GM12878	blood:	n/a	n/a
49	POLR2A	chr12:56439930-56440411	K562	blood:	n/a	n/a
50	POLR2A	chr12:56438684-56441201	MCF-7	breast:	n/a	n/a

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56438264..56440489-chr12:56580278..56583013,2	K562	blood:
2	chr12:56435284..56441183-chr12:56476886..56481327,8	MCF-7	breast:
3	chr12:56433777..56443620-chr12:56502225..56514736,38	MCF-7	breast:
4	chr12:56409589..56411250-chr12:56439300..56441018,2	MCF-7	breast:
5	chr12:56434034..56442629-chr12:56495467..56501430,16	MCF-7	breast:
6	chr12:56119294..56126638-chr12:56434111..56441706,13	K562	blood:
7	chr12:56390919..56392960-chr12:56439396..56441084,2	K562	blood:
8	chr12:56434164..56442518-chr12:56471459..56476251,24	MCF-7	breast:
9	chr12:56438543..56440951-chr12:56480684..56483081,2	K562	blood:
10	chr12:56433873..56442113-chr12:56515349..56524351,14	K562	blood:
11	chr12:56431889..56443161-chr12:56494616..56500426,22	MCF-7	breast:
12	chr12:56434006..56443603-chr12:56507645..56514884,44	K562	blood:
13	chr12:56434525..56442579-chr12:56469196..56475242,12	K562	blood:
14	chr12:56438101..56442665-chr12:56471305..56476433,10	MCF-7	breast:
15	chr12:56434544..56443137-chr12:56494029..56505252,21	K562	blood:
16	chr12:56435618..56442072-chr12:56498381..56502676,10	K562	blood:
17	chr12:56320184..56328034-chr12:56431937..56442233,20	MCF-7	breast:
18	chr12:56433331..56443603-chr12:56506173..56514581,35	K562	blood:
19	chr12:56438865..56441030-chr12:56491226..56492795,2	MCF-7	breast:
20	chr12:56439022..56443137-chr12:56446581..56450430,4	MCF-7	breast:
21	chr12:56395813..56397827-chr12:56439578..56442560,2	K562	blood:
22	chr12:56353631..56355225-chr12:56438700..56441265,2	MCF-7	breast:
23	chr12:56434525..56442579-chr12:56471686..56475431,10	K562	blood:
24	chr12:56388988..56394527-chr12:56433794..56442585,20	K562	blood:
25	chr12:56124914..56126638-chr12:56438630..56440550,2	K562	blood:
26	chr12:56438470..56440539-chr12:56581199..56583152,2	MCF-7	breast:
27	chr12:56433908..56446518-chr12:56506026..56517165,55	MCF-7	breast:
28	chr12:56438693..56440512-chr12:56581883..56583749,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257449	TF binding region
ENSG00000135482	Chromatin interaction
ENSG00000257411	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000257384	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000257553	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000139613	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11171736	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11171753	1.00[TSI][hapmap]
rs11171760	1.00[EUR][1000 genomes]
rs11171777	1.00[TSI][hapmap]
rs11834728	1.00[TSI][hapmap]
rs11837267	1.00[EUR][1000 genomes]
rs12298822	1.00[EUR][1000 genomes]
rs12306670	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12308473	1.00[EUR][1000 genomes]
rs12320265	1.00[TSI][hapmap]
rs1581007	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1619653	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1689507	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1689516	0.85[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1701705	0.85[ASW][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1702870	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1702871	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1702875	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17852368	1.00[EUR][1000 genomes]
rs2450101	1.00[EUR][1000 genomes]
rs2452822	0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2452826	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2456445	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2456446	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2456969	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2463365	1.00[TSI][hapmap]
rs2629453	1.00[EUR][1000 genomes]
rs2695783	1.00[TSI][hapmap]
rs2695784	1.00[TSI][hapmap]
rs28546848	1.00[EUR][1000 genomes]
rs2930788	1.00[TSI][hapmap]
rs56163805	1.00[EUR][1000 genomes]
rs59499104	1.00[EUR][1000 genomes]
rs703823	1.00[TSI][hapmap]
rs705706	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7136420	1.00[TSI][hapmap]
rs7301099	0.80[MKK][hapmap]
rs7309340	0.85[AFR][1000 genomes]
rs73340385	1.00[EUR][1000 genomes]
rs73340390	1.00[EUR][1000 genomes]
rs7397951	1.00[EUR][1000 genomes]
rs7489249	1.00[TSI][hapmap]
rs772917	0.96[AFR][1000 genomes]
rs772924	0.88[AFR][1000 genomes]
rs772925	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs773118	0.91[AFR][1000 genomes]
rs773654	1.00[EUR][1000 genomes]
rs773658	1.00[TSI][hapmap]
rs773659	1.00[TSI][hapmap]
rs773663	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7967464	1.00[EUR][1000 genomes]
rs7975486	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7977521	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs808896	0.85[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs808905	0.85[AFR][1000 genomes]
rs9645818	0.88[AFR][1000 genomes]
rs9738150	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv1067906	chr12:56424828-56445284	Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56437000-56447200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:56437000-56472800	Weak transcription	Right Atrium	heart
3	chr12:56437200-56440800	Weak transcription	Fetal Heart	heart
4	chr12:56437400-56440400	Strong transcription	Primary B cells from cord blood	blood
5	chr12:56437400-56440600	Strong transcription	Brain Angular Gyrus	brain
6	chr12:56437400-56440800	Strong transcription	Fetal Stomach	stomach
7	chr12:56437600-56440400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:56437600-56440400	Strong transcription	Brain Cingulate Gyrus	brain
9	chr12:56437600-56440400	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr12:56437600-56440600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr12:56437600-56440800	Strong transcription	Fetal Thymus	thymus
12	chr12:56437800-56440400	Strong transcription	Primary T cells from cord blood	blood
13	chr12:56437800-56440400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:56437800-56440400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:56437800-56440400	Strong transcription	Brain Germinal Matrix	brain
16	chr12:56437800-56440400	Strong transcription	Brain Hippocampus Middle	brain
17	chr12:56437800-56440400	Weak transcription	Small Intestine	intestine
18	chr12:56437800-56440400	Strong transcription	HMEC	breast
19	chr12:56437800-56440600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr12:56437800-56440600	Strong transcription	A549	lung
21	chr12:56437800-56440800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:56437800-56440800	Weak transcription	Gastric	stomach
23	chr12:56437800-56450000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:56438000-56440400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:56438000-56440600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr12:56438000-56440800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:56438000-56442000	Weak transcription	Fetal Kidney	kidney
28	chr12:56438000-56442400	Weak transcription	Fetal Brain Male	brain
29	chr12:56438600-56440600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:56438800-56440800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr12:56439000-56440400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:56439200-56440800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:56439200-56440800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:56439200-56440800	Weak transcription	Right Ventricle	heart
35	chr12:56439400-56440400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:56439400-56440400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr12:56439400-56440400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:56439400-56440600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr12:56439400-56440600	Genic enhancers	K562	blood
40	chr12:56439400-56440800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:56439400-56440800	Weak transcription	Stomach Mucosa	stomach
42	chr12:56439400-56441000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr12:56439400-56441000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:56439400-56441000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:56439400-56441000	Weak transcription	Esophagus	oesophagus
46	chr12:56439400-56441000	Weak transcription	Ovary	ovary
47	chr12:56439400-56441000	Weak transcription	Pancreas	Pancrea
48	chr12:56439400-56441000	Weak transcription	Psoas Muscle	Psoas
49	chr12:56439400-56441000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:56439400-56441200	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links