Variant report

Variant	rs10259673
Chromosome Location	chr7:138177239-138177240
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	chr7:138177103-138177375	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:138177117-138178124	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000234995	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10216085	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10224459	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10224559	0.94[AFR][1000 genomes]
rs10226487	0.94[AFR][1000 genomes]
rs10231698	0.83[YRI][hapmap];0.94[AFR][1000 genomes]
rs10232597	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10234810	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10236859	0.94[AFR][1000 genomes]
rs10237069	0.94[AFR][1000 genomes]
rs10237544	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10237720	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10239129	0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs10239202	0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10239932	0.94[AFR][1000 genomes]
rs10241288	0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10241942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10242105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10243069	0.94[AFR][1000 genomes]
rs10245088	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10248604	0.94[AFR][1000 genomes]
rs10253989	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10254440	0.94[AFR][1000 genomes]
rs10254935	0.91[AFR][1000 genomes]
rs10256094	0.94[AFR][1000 genomes]
rs10256358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10256619	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10261236	0.82[AFR][1000 genomes]
rs10267577	0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10268912	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10272478	0.94[AFR][1000 genomes]
rs10277465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10278741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10281429	0.82[AFR][1000 genomes]
rs10281487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1073255	0.94[AFR][1000 genomes]
rs13438570	0.94[AFR][1000 genomes]
rs28361932	0.82[AFR][1000 genomes]
rs28380017	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28392567	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28407067	0.94[AFR][1000 genomes]
rs28498774	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28502705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28534820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28584756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28598597	0.94[AFR][1000 genomes]
rs28608602	0.94[AFR][1000 genomes]
rs28673291	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28688534	0.94[AFR][1000 genomes]
rs28694658	0.94[AFR][1000 genomes]
rs28706910	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28707292	0.94[AFR][1000 genomes]
rs28714460	0.82[AFR][1000 genomes]
rs28729263	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28762120	0.91[AFR][1000 genomes]
rs28764878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28816768	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28822161	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2883144	1.00[AMR][1000 genomes]
rs3847123	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3847124	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4329204	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6947993	1.00[AMR][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	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831153	chr7:138078179-138265648	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1030956	chr7:138163169-138579519	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv981589	chr7:138163846-138177455	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138147200-138183800	Weak transcription	Primary B cells from cord blood	blood
2	chr7:138147200-138189000	Weak transcription	Thymus	Thymus
3	chr7:138149800-138188600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:138153800-138184200	Weak transcription	Fetal Stomach	stomach
5	chr7:138155200-138184200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:138157600-138191400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:138160600-138182200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:138161800-138195800	Weak transcription	Fetal Brain Female	brain
9	chr7:138163600-138183400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:138163600-138184000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:138163600-138184200	Weak transcription	Aorta	Aorta
12	chr7:138163600-138184200	Weak transcription	Fetal Thymus	thymus
13	chr7:138164000-138191400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:138164000-138199800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:138164400-138184200	Weak transcription	Ovary	ovary
16	chr7:138165000-138192000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:138165600-138184000	Weak transcription	Primary T cells from cord blood	blood
18	chr7:138166600-138184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr7:138167000-138177800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:138168000-138181400	Weak transcription	Fetal Intestine Small	intestine
21	chr7:138168000-138196200	Weak transcription	Left Ventricle	heart
22	chr7:138168200-138178200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:138168800-138184200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:138169000-138190200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr7:138172800-138184400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:138173800-138183400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr7:138174600-138184200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:138175200-138201200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr7:138175400-138177400	Genic enhancers	HepG2	liver
30	chr7:138175400-138177600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr7:138175400-138185200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:138175800-138177600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:138175800-138183000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:138176000-138177600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:138176000-138180000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:138176000-138183400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr7:138176200-138178400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr7:138176200-138180000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:138176200-138184000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr7:138176200-138184000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr7:138176200-138184000	Weak transcription	Dnd41	blood
42	chr7:138176400-138177600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr7:138176400-138178400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr7:138176400-138179400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr7:138176400-138186800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr7:138176600-138177400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr7:138176600-138183800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr7:138176600-138184000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr7:138176600-138184000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr7:138176600-138190200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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