Variant report

Variant	rs34303864
Chromosome Location	chr12:56439373-56439374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:96)
CpG islands
(count:0)
Chromatin interactive
region (count:37)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:96 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56438995-56439699	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:56438456-56440437	K562	blood:	n/a	n/a
3	POLR2A	chr12:56438381-56439837	U87	brain:	n/a	n/a
4	MTA3	chr12:56438824-56440626	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:56439102-56439392	HepG2	liver:	n/a	n/a
6	CHD2	chr12:56439233-56439626	H1-hESC	embryonic stem cell:	n/a	n/a
7	BCLAF1	chr12:56439232-56439671	GM12878	blood:	n/a	chr12:56439388-56439397
8	BCLAF1	chr12:56439122-56439717	GM12878	blood:	n/a	chr12:56439388-56439397
9	POLR2A	chr12:56438336-56439838	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:56439141-56439768	GM12892	blood:	n/a	n/a
11	POLR2A	chr12:56438459-56440686	GM12891	blood:	n/a	n/a
12	POLR2A	chr12:56438442-56440629	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr12:56437986-56441151	GM12892	blood:	n/a	n/a
14	POLR2A	chr12:56438483-56439780	K562	blood:	n/a	n/a
15	HEY1	chr12:56439144-56439642	HepG2	liver:	n/a	n/a
16	POLR2A	chr12:56438901-56439486	K562	blood:	n/a	n/a
17	POLR2A	chr12:56438153-56441424	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:56438806-56439782	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr12:56438344-56440599	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr12:56439306-56439764	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:56438494-56440643	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr12:56438473-56440539	H1-hESC	embryonic stem cell:	n/a	n/a
23	SPI1	chr12:56439260-56439500	GM12891	blood:	n/a	chr12:56439387-56439396 chr12:56439384-56439397 chr12:56439391-56439400 chr12:56439385-56439398
24	POLR2A	chr12:56438731-56439800	HL-60	blood:	n/a	n/a
25	POLR2A	chr12:56438226-56441381	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr12:56438594-56439771	K562	blood:	n/a	n/a
27	POLR2A	chr12:56438236-56441303	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr12:56438333-56439833	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:56438454-56440739	U87	brain:	n/a	n/a
30	POLR2A	chr12:56439231-56439640	PBDE	blood:	n/a	n/a
31	POLR2A	chr12:56439043-56439692	Raji	blood:	n/a	n/a
32	POLR2A	chr12:56438490-56439805	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:56438852-56441257	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr12:56438745-56440930	HepG2	liver:	n/a	n/a
35	ATF2	chr12:56439187-56439577	H1-hESC	embryonic stem cell:	n/a	n/a
36	CHD2	chr12:56439357-56439390	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr12:56438157-56441263	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:56439133-56439587	A549	lung:	n/a	n/a
39	POLR2A	chr12:56438282-56439839	K562	blood:	n/a	n/a
40	POLR2A	chr12:56438341-56440799	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr12:56438339-56441188	GM12892	blood:	n/a	n/a
42	POLR2A	chr12:56439077-56439796	HepG2	liver:	n/a	n/a
43	POLR2A	chr12:56438416-56440547	K562	blood:	n/a	n/a
44	HEY1	chr12:56439098-56439627	HepG2	liver:	n/a	n/a
45	POLR2A	chr12:56438454-56441401	U87	brain:	n/a	n/a
46	POLR2A	chr12:56438398-56439820	GM12891	blood:	n/a	n/a
47	PML	chr12:56438570-56441338	GM12878	blood:	n/a	n/a
48	POLR2A	chr12:56438755-56439962	HUVEC	blood vessel:	n/a	n/a
49	NFATC1	chr12:56438811-56439864	GM12878	blood:	n/a	n/a
50	HEY1	chr12:56439141-56439761	K562	blood:	n/a	n/a

No data

(count:37 , 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	chr12:56320043..56321671-chr12:56437761..56440177,2	K562	blood:
6	chr12:56361700..56363713-chr12:56435997..56439581,3	MCF-7	breast:
7	chr12:56434034..56442629-chr12:56495467..56501430,16	MCF-7	breast:
8	chr12:56398217..56408038-chr12:56433794..56439966,15	K562	blood:
9	chr12:56119294..56126638-chr12:56434111..56441706,13	K562	blood:
10	chr12:56434164..56442518-chr12:56471459..56476251,24	MCF-7	breast:
11	chr12:56437992..56439705-chr12:56691298..56693629,2	K562	blood:
12	chr12:56438543..56440951-chr12:56480684..56483081,2	K562	blood:
13	chr12:56433873..56442113-chr12:56515349..56524351,14	K562	blood:
14	chr12:56438679..56439417-chr20:30194678..30195414,2	Hela-S3	cervix:
15	chr12:56431889..56443161-chr12:56494616..56500426,22	MCF-7	breast:
16	chr12:56434006..56443603-chr12:56507645..56514884,44	K562	blood:
17	chr12:56434525..56442579-chr12:56469196..56475242,12	K562	blood:
18	chr12:56438101..56442665-chr12:56471305..56476433,10	MCF-7	breast:
19	chr12:56434544..56443137-chr12:56494029..56505252,21	K562	blood:
20	chr12:56435618..56442072-chr12:56498381..56502676,10	K562	blood:
21	chr12:56320184..56328034-chr12:56431937..56442233,20	MCF-7	breast:
22	chr12:56324080..56326028-chr12:56437410..56439658,2	K562	blood:
23	chr12:56433331..56443603-chr12:56506173..56514581,35	K562	blood:
24	chr12:56437312..56439402-chr12:56550075..56552742,2	MCF-7	breast:
25	chr12:56328007..56330555-chr12:56437110..56439690,2	MCF-7	breast:
26	chr12:56438865..56441030-chr12:56491226..56492795,2	MCF-7	breast:
27	chr12:56439022..56443137-chr12:56446581..56450430,4	MCF-7	breast:
28	chr12:56437997..56440077-chr12:56556609..56558921,2	K562	blood:
29	chr12:56353631..56355225-chr12:56438700..56441265,2	MCF-7	breast:
30	chr12:56434525..56442579-chr12:56471686..56475431,10	K562	blood:
31	chr12:56388988..56394527-chr12:56433794..56442585,20	K562	blood:
32	chr12:56386022..56392601-chr12:56434180..56439537,11	MCF-7	breast:
33	chr12:56437402..56439705-chr12:56691985..56693629,2	K562	blood:
34	chr12:56124914..56126638-chr12:56438630..56440550,2	K562	blood:
35	chr12:56438470..56440539-chr12:56581199..56583152,2	MCF-7	breast:
36	chr12:56433908..56446518-chr12:56506026..56517165,55	MCF-7	breast:
37	chr12:56438693..56440512-chr12:56581883..56583749,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257449	TF binding region
ENSG00000092841	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000257384	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000257553	Chromatin interaction
ENSG00000264395	Chromatin interaction
ENSG00000257411	Chromatin interaction
ENSG00000196465	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11171713	0.93[AMR][1000 genomes]
rs11171714	0.93[AMR][1000 genomes]
rs11171715	0.82[AMR][1000 genomes]
rs12099979	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12810011	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12815302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12815387	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12815488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12817471	0.85[EUR][1000 genomes]
rs12817765	0.93[AMR][1000 genomes]
rs12818756	1.00[EUR][1000 genomes]
rs12831468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1614219	0.98[EUR][1000 genomes]
rs1689511	0.95[EUR][1000 genomes]
rs1701706	0.91[EUR][1000 genomes]
rs17118206	0.93[AMR][1000 genomes]
rs17118208	0.93[AMR][1000 genomes]
rs17118262	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131569	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2456972	0.98[EUR][1000 genomes]
rs2658479	0.94[EUR][1000 genomes]
rs34071823	0.93[AMR][1000 genomes]
rs34228181	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34273234	0.87[AMR][1000 genomes]
rs34406511	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34485293	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34507011	0.91[EUR][1000 genomes]
rs34602183	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34650555	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34921584	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34962186	0.93[AMR][1000 genomes]
rs35485002	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35662491	0.85[EUR][1000 genomes]
rs35666826	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs35961650	0.94[EUR][1000 genomes]
rs4759022	1.00[EUR][1000 genomes]
rs4759239	0.94[EUR][1000 genomes]
rs56073151	1.00[ASN][1000 genomes]
rs67594137	0.87[AMR][1000 genomes]
rs71447768	0.93[AMR][1000 genomes]
rs71459326	0.93[AMR][1000 genomes]
rs71459327	0.93[AMR][1000 genomes]
rs71459334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459336	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71459339	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459342	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7298818	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7300772	0.98[EUR][1000 genomes]
rs772919	0.89[EUR][1000 genomes]
rs772922	0.91[EUR][1000 genomes]
rs772923	0.92[EUR][1000 genomes]
rs773115	0.94[EUR][1000 genomes]
rs7963590	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7977537	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34303864	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs34303864	SUOX	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56436600-56439400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56437000-56439400	Strong transcription	Lung	lung
3	chr12:56437000-56439600	Strong transcription	Left Ventricle	heart
4	chr12:56437000-56440000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:56437000-56447200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:56437000-56472800	Weak transcription	Right Atrium	heart
7	chr12:56437200-56439400	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr12:56437200-56439400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:56437200-56439400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:56437200-56439400	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:56437200-56439600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:56437200-56439600	Strong transcription	Aorta	Aorta
13	chr12:56437200-56439600	Strong transcription	Colon Smooth Muscle	Colon
14	chr12:56437200-56439600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:56437200-56439600	Strong transcription	Placenta Amnion	Placenta Amnion
16	chr12:56437200-56439800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:56437200-56440800	Weak transcription	Fetal Heart	heart
18	chr12:56437400-56439400	Strong transcription	Esophagus	oesophagus
19	chr12:56437400-56439600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:56437400-56439800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:56437400-56439800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:56437400-56439800	Strong transcription	Brain Substantia Nigra	brain
23	chr12:56437400-56440400	Strong transcription	Primary B cells from cord blood	blood
24	chr12:56437400-56440600	Strong transcription	Brain Angular Gyrus	brain
25	chr12:56437400-56440800	Strong transcription	Fetal Stomach	stomach
26	chr12:56437600-56439400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:56437600-56439400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:56437600-56439400	Strong transcription	Rectal Smooth Muscle	rectum
29	chr12:56437600-56439400	Strong transcription	Stomach Mucosa	stomach
30	chr12:56437600-56439600	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr12:56437600-56439600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr12:56437600-56439600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:56437600-56439600	Strong transcription	Adipose Nuclei	Adipose
34	chr12:56437600-56439600	Strong transcription	Liver	Liver
35	chr12:56437600-56439600	Strong transcription	Brain Anterior Caudate	brain
36	chr12:56437600-56439600	Strong transcription	Fetal Muscle Leg	muscle
37	chr12:56437600-56439600	Strong transcription	NH-A	brain
38	chr12:56437600-56439800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:56437600-56439800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:56437600-56439800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:56437600-56439800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr12:56437600-56440200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr12:56437600-56440400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:56437600-56440400	Strong transcription	Brain Cingulate Gyrus	brain
45	chr12:56437600-56440400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr12:56437600-56440600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr12:56437600-56440800	Strong transcription	Fetal Thymus	thymus
48	chr12:56437800-56439400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:56437800-56439400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:56437800-56439400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

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