Variant report

Variant	rs2302155
Chromosome Location	chr2:234754506-234754507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:234754438-234754777	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:234745990-234762655	K562	blood:	n/a	n/a
3	SPI1	chr2:234754374-234754741	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:234754297-234754555	K562	blood:	n/a	n/a
5	SPI1	chr2:234754404-234754704	GM12891	blood:	n/a	n/a
6	SPI1	chr2:234754309-234754697	GM12891	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP40-4	chr2:234754374-234754781	NONHSAT077519

Variant related genes	Relation type
HJURP	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1003540	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10166942	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10170399	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10187654	0.83[ASN][1000 genomes]
rs10929309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929312	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10929314	0.93[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11563063	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11563066	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11563227	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11892538	0.86[JPT][hapmap]
rs12997802	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13016127	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13016553	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1392606	0.96[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1965629	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1985366	0.80[ASN][1000 genomes]
rs2159200	0.89[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286431	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362290	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs3732215	0.96[CEU][hapmap];0.91[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4663983	0.81[ASN][1000 genomes]
rs6709005	0.86[JPT][hapmap]
rs6738979	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6760630	0.83[ASN][1000 genomes]
rs7567475	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs887061	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs917432	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs917433	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs917434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968402	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs990418	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	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
4	nsv1008316	chr2:234728911-234758539	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 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	chr2:234743000-234758600	Strong transcription	Fetal Intestine Large	intestine
24	chr2:234743000-234759400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:234743000-234760000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:234743000-234760000	Strong transcription	HMEC	breast
27	chr2:234743000-234760800	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr2:234743000-234760800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:234743000-234761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:234743200-234760200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:234743200-234760600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:234743200-234760600	Strong transcription	Fetal Muscle Leg	muscle
33	chr2:234743400-234759400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:234743800-234759800	Strong transcription	Osteobl	bone
35	chr2:234744000-234760400	Strong transcription	K562	blood
36	chr2:234744000-234762400	Weak transcription	Small Intestine	intestine
37	chr2:234744200-234755400	Weak transcription	Fetal Brain Male	brain
38	chr2:234744600-234762000	Weak transcription	Colonic Mucosa	Colon
39	chr2:234747800-234760400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:234748000-234759200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:234748000-234760400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr2:234748000-234760400	Strong transcription	Fetal Stomach	stomach
43	chr2:234748200-234758400	Strong transcription	Fetal Thymus	thymus
44	chr2:234748200-234759000	Genic enhancers	Dnd41	blood
45	chr2:234748200-234760600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr2:234748400-234760600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:234748600-234762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:234748800-234756600	Strong transcription	HSMM	muscle
49	chr2:234748800-234757600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr2:234749000-234755000	Strong transcription	NH-A	brain

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