Variant report

Variant	rs2242036
Chromosome Location	chr2:100010685-100010686
allele	A/G
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	chr2:100010558-100010801	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:100010547-100011050	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:100010038-100028424	K562	blood:	n/a	n/a

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:

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

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1011633	0.88[JPT][hapmap]
rs10207981	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs1053544	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs11123775	0.88[JPT][hapmap]
rs11123785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884686	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs11892441	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs11899745	0.88[JPT][hapmap]
rs12053519	0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12053566	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12233086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12233126	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]
rs12464785	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1451245	0.82[ASW][hapmap];0.91[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1584647	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs1584648	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs17022433	0.88[JPT][hapmap]
rs17022564	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs17022629	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2200578	0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2290255	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2290257	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2290261	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2309617	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs28369925	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28369944	0.80[EUR][1000 genomes]
rs28382892	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28382949	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749087	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs3791212	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs3791213	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3792135	0.82[ASW][hapmap];0.91[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3792136	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3792137	0.88[JPT][hapmap]
rs3792138	0.80[MEX][hapmap]
rs3792142	0.87[JPT][hapmap]
rs4143760	0.88[JPT][hapmap]
rs4851206	0.88[JPT][hapmap]
rs57043099	0.80[AMR][1000 genomes]
rs58123905	0.83[EUR][1000 genomes]
rs58766196	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59360884	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60572342	0.83[AMR][1000 genomes]
rs60730619	0.80[EUR][1000 genomes]
rs61577246	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6715321	0.88[JPT][hapmap]
rs6722617	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs6727483	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6728175	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6728936	0.84[EUR][1000 genomes]
rs717454	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs72954262	0.86[EUR][1000 genomes]
rs72954283	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72954284	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72954287	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72956308	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72956312	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72956317	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72956346	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72956387	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72958366	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72958380	0.81[AMR][1000 genomes]
rs7563462	0.88[JPT][hapmap]
rs7585019	0.88[JPT][hapmap]
rs7593274	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs7597141	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs769105	0.88[JPT][hapmap]
rs896248	0.86[JPT][hapmap]
rs896249	0.88[JPT][hapmap]
rs9941566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2242036	COX5B	cis	parietal	SCAN
rs2242036	TSGA10	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99978200-100011800	Weak transcription	Esophagus	oesophagus
2	chr2:99983200-100013600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:99990000-100012200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:99990200-100010800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:99990600-100010800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:99990600-100010800	Weak transcription	Spleen	Spleen
7	chr2:99994200-100010800	Weak transcription	Fetal Brain Male	brain
8	chr2:99994200-100011400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:99997200-100011000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:99999400-100056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:100000000-100014800	Weak transcription	Psoas Muscle	Psoas
12	chr2:100001000-100022000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:100003600-100010800	Weak transcription	Lung	lung
14	chr2:100003600-100011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:100004800-100023000	Strong transcription	Primary B cells from cord blood	blood
16	chr2:100004800-100044800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:100005200-100049800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:100005400-100020000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:100005600-100045400	Strong transcription	Primary T cells from cord blood	blood
20	chr2:100005800-100016600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:100005800-100019600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:100005800-100019600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:100005800-100045200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr2:100005800-100062600	Strong transcription	Dnd41	blood
25	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:100006000-100012200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:100006000-100019000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:100006000-100019200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:100006000-100019200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:100006000-100019600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:100006000-100023400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:100006000-100026200	Strong transcription	HUVEC	blood vessel
33	chr2:100006000-100034200	Strong transcription	GM12878-XiMat	blood
34	chr2:100006000-100046400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:100006000-100049600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:100006000-100050800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:100006000-100051000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr2:100006200-100017800	Strong transcription	Hela-S3	cervix
40	chr2:100006200-100019000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:100006200-100019800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:100006200-100023600	Strong transcription	Fetal Thymus	thymus
43	chr2:100006200-100028600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:100006200-100046400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:100006200-100051400	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:100006400-100016400	Strong transcription	A549	lung
47	chr2:100006400-100019400	Strong transcription	Osteobl	bone
48	chr2:100006400-100020200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:100006400-100022600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:100006400-100023000	Strong transcription	Primary hematopoietic stem cells	blood

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