Variant report

Variant	rs3792150
Chromosome Location	chr2:100041849-100041850
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	FOS	chr2:100041515-100041865	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr2:100041513-100041865	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:100041605-100041853	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr2:100041520-100041854	MCF10A-Er-Src	breast:	n/a	n/a
5	NFIC	chr2:100041469-100042004	SK-N-SH	brain:	n/a	n/a
6	FOS	chr2:100041564-100041857	HUVEC	blood vessel:	n/a	n/a
7	STAT3	chr2:100041596-100041854	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr2:100041531-100041871	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr2:100041512-100041862	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
REV1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10496336	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11885942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887935	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11893359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11896520	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12466114	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12474305	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12479064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17760953	0.81[YRI][hapmap]
rs1823569	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1922624	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2141907	0.86[EUR][1000 genomes]
rs2305352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28369945	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28369960	0.80[ASN][1000 genomes]
rs28382977	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792143	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4341989	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851203	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851207	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4851210	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61436115	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62153852	0.84[EUR][1000 genomes]
rs62155769	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62155807	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6714650	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs737094	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[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	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	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
3	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
4	nsv1014161	chr2:100021040-100063406	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3792150	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99999400-100056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:100004800-100044800	Strong transcription	Primary T helper cells PMA-I stimulated	--
3	chr2:100005200-100049800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:100005600-100045400	Strong transcription	Primary T cells from cord blood	blood
5	chr2:100005800-100045200	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr2:100005800-100062600	Strong transcription	Dnd41	blood
7	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:100006000-100046400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:100006000-100049600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:100006000-100050800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:100006000-100051000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:100006200-100046400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr2:100006200-100051400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:100006400-100046600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:100006600-100042600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr2:100009000-100045000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr2:100009800-100050000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:100020600-100051400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:100020800-100050200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:100021000-100051800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:100021200-100050800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:100021200-100077800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:100021400-100049200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:100021400-100050800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:100022000-100047600	Weak transcription	Stomach Mucosa	stomach
27	chr2:100022000-100050000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:100022000-100054800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:100022200-100059000	Strong transcription	Liver	Liver
30	chr2:100024000-100046600	Strong transcription	Fetal Intestine Large	intestine
31	chr2:100024000-100050000	Strong transcription	HepG2	liver
32	chr2:100024400-100048400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:100024400-100051400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:100024800-100042000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr2:100025800-100049000	Strong transcription	Fetal Thymus	thymus
36	chr2:100026000-100048800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:100026800-100042000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr2:100029000-100045000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:100030800-100047400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:100031800-100045200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:100032600-100078000	Weak transcription	Psoas Muscle	Psoas
42	chr2:100034000-100055200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:100034200-100043800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:100034200-100044400	Weak transcription	Pancreas	Pancrea
45	chr2:100034200-100055000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:100034200-100088800	Weak transcription	Small Intestine	intestine
47	chr2:100035600-100045600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:100035800-100042400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:100035800-100045600	Strong transcription	K562	blood
50	chr2:100036000-100045000	Strong transcription	Fetal Muscle Leg	muscle

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