Variant report

Variant	rs11562956
Chromosome Location	chr2:234759164-234759165
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:234758866-234759315	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:234758407-234759188	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:234758586-234759725	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr2:234758532-234759524	K562	blood:	n/a	n/a
5	POLR2A	chr2:234756666-234759708	PBDE	blood:	n/a	n/a
6	POLR2A	chr2:234755154-234760215	U87	brain:	n/a	n/a
7	POLR2A	chr2:234755022-234759760	K562	blood:	n/a	n/a
8	POLR2A	chr2:234756132-234759205	K562	blood:	n/a	n/a
9	POLR2A	chr2:234757697-234759829	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:234756158-234759257	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr2:234745990-234762655	K562	blood:	n/a	n/a
12	POLR2A	chr2:234758276-234759733	K562	blood:	n/a	n/a
13	POLR2A	chr2:234754982-234760241	PANC-1	pancreas:	n/a	n/a
14	CCNT2	chr2:234759057-234759257	K562	blood:	n/a	n/a
15	POLR2A	chr2:234757285-234759804	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:234755167-234759670	A549	lung:	n/a	n/a
17	POLR2A	chr2:234755017-234760215	U87	brain:	n/a	n/a
18	POLR2A	chr2:234758416-234759794	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:234758197..234760837-chr2:234836027..234838488,2	K562	blood:
2	chr2:234753471..234756128-chr2:234758714..234761959,3	MCF-7	breast:
3	chr2:234747927..234752617-chr2:234757241..234760452,5	MCF-7	breast:

No data

Variant related genes	Relation type
HJURP	TF binding region
ENSG00000123485	Chromatin interaction
ENSG00000144481	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10490009	0.93[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs11562977	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11563011	0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11563068	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11563214	0.85[YRI][hapmap]
rs11563218	0.85[YRI][hapmap];0.91[AMR][1000 genomes]
rs11563226	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11563229	0.88[ASN][1000 genomes]
rs12617866	0.85[YRI][hapmap]
rs12620352	0.85[YRI][hapmap]
rs16849914	0.87[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2362291	0.85[YRI][hapmap];0.91[AMR][1000 genomes]
rs28900703	0.87[CHB][hapmap]
rs28900710	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs28900712	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28900713	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28900727	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs28900728	0.87[ASN][1000 genomes]
rs28900729	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs28900980	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs28900981	0.87[ASN][1000 genomes]
rs28901579	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs28901591	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs28901600	0.91[AMR][1000 genomes]
rs28901610	0.85[YRI][hapmap]
rs28901618	0.85[YRI][hapmap]
rs28901630	0.85[YRI][hapmap]
rs28901637	0.85[YRI][hapmap]
rs28901868	0.85[YRI][hapmap]
rs3771334	0.83[AMR][1000 genomes]
rs3806588	0.93[CHB][hapmap]
rs4663343	0.85[YRI][hapmap]
rs4663989	0.85[YRI][hapmap]
rs6754410	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7602303	0.85[YRI][hapmap]
rs9789366	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9789398	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9789675	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv876023	chr2:234726154-234763137	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234736400-234762600	Weak transcription	Right Atrium	heart
2	chr2:234738200-234762000	Weak transcription	Esophagus	oesophagus
3	chr2:234740000-234760000	Strong transcription	Thymus	Thymus
4	chr2:234740200-234761000	Weak transcription	Primary B cells from cord blood	blood
5	chr2:234740400-234762200	Weak transcription	Primary T cells from cord blood	blood
6	chr2:234741200-234759800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:234741800-234762000	Weak transcription	Gastric	stomach
8	chr2:234742000-234759600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr2:234742200-234759400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:234742200-234760400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:234742200-234762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:234742600-234759600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:234742600-234759800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:234742600-234760400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:234742600-234760600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:234742600-234760600	Strong transcription	NHEK	skin
17	chr2:234742600-234760800	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr2:234742800-234759800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:234742800-234760400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:234742800-234760600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:234742800-234760600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:234742800-234760800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:234743000-234759400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:234743000-234760000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:234743000-234760000	Strong transcription	HMEC	breast
26	chr2:234743000-234760800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr2:234743000-234760800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:234743000-234761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:234743200-234760200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:234743200-234760600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:234743200-234760600	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:234743400-234759400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:234743800-234759800	Strong transcription	Osteobl	bone
34	chr2:234744000-234760400	Strong transcription	K562	blood
35	chr2:234744000-234762400	Weak transcription	Small Intestine	intestine
36	chr2:234744600-234762000	Weak transcription	Colonic Mucosa	Colon
37	chr2:234747800-234760400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:234748000-234759200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:234748000-234760400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:234748000-234760400	Strong transcription	Fetal Stomach	stomach
41	chr2:234748200-234760600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr2:234748400-234760600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:234748600-234762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:234749200-234759800	Strong transcription	HepG2	liver
45	chr2:234749200-234760400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:234749200-234760400	Strong transcription	Hela-S3	cervix
47	chr2:234749200-234761600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr2:234749400-234759400	Strong transcription	HUVEC	blood vessel
49	chr2:234749400-234760600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:234750600-234761400	Weak transcription	Fetal Brain Female	brain

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