Variant report

Variant	rs10179923
Chromosome Location	chr2:111609690-111609691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111589730..111592608-chr2:111607480..111611247,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10169852	0.82[CEU][hapmap]
rs10180020	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180446	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12476878	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12711785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13019266	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1533295	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1533298	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1533300	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1554006	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1969232	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1969233	0.81[ASN][1000 genomes]
rs2341873	0.86[CEU][hapmap]
rs2612698	0.86[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs2612700	0.91[CEU][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs4848317	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs4849134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4849135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849155	0.86[CEU][hapmap];0.87[JPT][hapmap]
rs66782223	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7576541	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7588925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917154	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1008758	chr2:111415136-111626467	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv535890	chr2:111415136-111626467	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv997829	chr2:111486961-111780537	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv834330	chr2:111593290-111789447	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv874840	chr2:111605245-111695479	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1004949	chr2:111607532-111780719	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1002568	chr2:111607532-111781442	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111596400-111611600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:111597000-111611400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:111601400-111611000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:111601800-111611600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:111604000-111611600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:111604600-111609800	Weak transcription	Primary B cells from cord blood	blood
7	chr2:111604800-111615800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:111605000-111611600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:111605600-111610200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr2:111608000-111618800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:111608200-111613000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:111608400-111610400	Enhancers	Dnd41	blood
13	chr2:111608400-111610800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:111608400-111611800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:111608400-111613400	Enhancers	Fetal Thymus	thymus
16	chr2:111608600-111612400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr2:111608600-111612600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:111608600-111612600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:111608800-111611800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr2:111608800-111612000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr2:111608800-111612000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr2:111609000-111609800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:111609000-111610000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:111609000-111611000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:111609000-111611800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:111609000-111612800	Enhancers	Primary T cells from cord blood	blood
27	chr2:111609200-111611200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr2:111609200-111611200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:111609200-111611600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:111609200-111611800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:111609200-111612400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr2:111609400-111610000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:111609400-111610600	Enhancers	Spleen	Spleen
34	chr2:111609400-111611000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:111609400-111612800	Enhancers	Thymus	Thymus
36	chr2:111609600-111609800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr2:111609600-111610200	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr2:111609600-111611000	Enhancers	Primary hematopoietic stem cells	blood

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