Variant report

Variant	rs12233126
Chromosome Location	chr2:100012200-100012201
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:100012124-100012521	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:100012150-100012494	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:100011412-100013175	MCF-7	breast:	n/a	n/a
4	POLR2A	chr2:100012135-100015082	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:100012150-100012486	K562	blood:	n/a	n/a
6	POLR2A	chr2:100011630-100017383	K562	blood:	n/a	n/a
7	POLR2A	chr2:100012064-100012565	GM12891	blood:	n/a	n/a
8	POLR2A	chr2:100011623-100012410	A549	lung:	n/a	n/a
9	POLR2A	chr2:100012188-100012599	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr2:100012127-100012621	K562	blood:	n/a	n/a
11	POLR2A	chr2:100012191-100012425	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr2:100012023-100012819	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr2:100012025-100012612	GM12878	blood:	n/a	n/a
14	FOSL2	chr2:100012052-100013471	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:100012114-100013069	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:100012177-100016656	GM12891	blood:	n/a	n/a
17	POLR2A	chr2:100012102-100016652	GM12878	blood:	n/a	n/a
18	RCOR1	chr2:100012132-100012344	K562	blood:	n/a	n/a
19	POLR2A	chr2:100010038-100028424	K562	blood:	n/a	n/a
20	POLR2A	chr2:100012107-100013589	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:100011960-100012500	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr2:100012148-100012501	K562	blood:	n/a	n/a
23	POLR2A	chr2:100011558-100023544	K562	blood:	n/a	n/a
24	POLR2A	chr2:100012093-100012441	GM12891	blood:	n/a	n/a
25	POLR2A	chr2:100012191-100012973	HepG2	liver:	n/a	n/a
26	CTCF	chr2:100012180-100012330	SK-N-SH_RA	brain:	n/a	n/a
27	POLR2A	chr2:100012038-100012500	GM12891	blood:	n/a	n/a
28	POLR2A	chr2:100011648-100013610	HepG2	liver:	n/a	n/a
29	POLR2A	chr2:100012039-100012508	HL-60	blood:	n/a	n/a
30	POLR2A	chr2:100011420-100016315	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:100010012..100012925-chr2:100019306..100020928,2	K562	blood:
2	chr2:100008715..100012637-chr2:100019428..100022260,4	K562	blood:
3	chr2:100010402..100012804-chr2:100013406..100016035,2	MCF-7	breast:

No data

Variant related genes	Relation type
EIF5B	TF binding region
ENSG00000273306	Chromatin interaction
ENSG00000158417	Chromatin interaction
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1011633	0.89[JPT][hapmap]
rs10207981	0.84[JPT][hapmap]
rs1053544	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs11123775	0.89[JPT][hapmap]
rs11123785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884686	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs11892441	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs11899745	0.89[JPT][hapmap]
rs12053519	1.00[JPT][hapmap]
rs12053566	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12233086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12464785	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs1451245	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1584647	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1584648	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs17022433	0.89[JPT][hapmap]
rs17022564	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs17022629	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2200578	1.00[JPT][hapmap]
rs2242036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290255	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs2290257	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2290261	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2309617	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs28369925	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28382892	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28382949	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749087	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3791212	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3791213	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3792135	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3792136	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3792137	0.89[JPT][hapmap]
rs3792142	0.88[JPT][hapmap]
rs4143760	0.89[JPT][hapmap]
rs4851206	0.89[JPT][hapmap]
rs57043099	0.80[AMR][1000 genomes]
rs58766196	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59360884	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60572342	0.83[AMR][1000 genomes]
rs61577246	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6715321	0.89[JPT][hapmap]
rs6722617	0.84[JPT][hapmap]
rs6727483	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6728175	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6728936	0.80[EUR][1000 genomes]
rs717454	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs72954262	0.82[EUR][1000 genomes]
rs72954283	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72954284	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72954287	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72956308	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72956312	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72956317	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72956346	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72956387	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72958366	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72958380	0.81[AMR][1000 genomes]
rs7563462	0.89[JPT][hapmap]
rs7585019	0.89[JPT][hapmap]
rs7593274	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs7597141	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs769105	0.89[JPT][hapmap]
rs896248	0.87[JPT][hapmap]
rs896249	0.89[JPT][hapmap]
rs9941566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv524466	chr2:99952086-100031551	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:130 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99983200-100013600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:99990000-100012200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:99999400-100056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:100000000-100014800	Weak transcription	Psoas Muscle	Psoas
5	chr2:100001000-100022000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:100004800-100023000	Strong transcription	Primary B cells from cord blood	blood
7	chr2:100004800-100044800	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:100005200-100049800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:100005400-100020000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:100005600-100045400	Strong transcription	Primary T cells from cord blood	blood
11	chr2:100005800-100016600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:100005800-100019600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:100005800-100019600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:100005800-100045200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr2:100005800-100062600	Strong transcription	Dnd41	blood
16	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:100006000-100012200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:100006000-100019000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:100006000-100019200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:100006000-100019200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:100006000-100019600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:100006000-100023400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:100006000-100026200	Strong transcription	HUVEC	blood vessel
24	chr2:100006000-100034200	Strong transcription	GM12878-XiMat	blood
25	chr2:100006000-100046400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:100006000-100049600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:100006000-100050800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr2:100006000-100051000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:100006200-100017800	Strong transcription	Hela-S3	cervix
31	chr2:100006200-100019000	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:100006200-100019800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:100006200-100023600	Strong transcription	Fetal Thymus	thymus
34	chr2:100006200-100028600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:100006200-100046400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:100006200-100051400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:100006400-100016400	Strong transcription	A549	lung
38	chr2:100006400-100019400	Strong transcription	Osteobl	bone
39	chr2:100006400-100020200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:100006400-100022600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:100006400-100023000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:100006400-100034200	Strong transcription	Fetal Brain Female	brain
43	chr2:100006400-100046600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:100006600-100013600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:100006600-100013800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:100006600-100015000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:100006600-100019000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:100006600-100019400	Strong transcription	Fetal Intestine Large	intestine
49	chr2:100006600-100019600	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr2:100006600-100019600	Strong transcription	Duodenum Mucosa	Duodenum

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