Variant report

Variant	rs10180446
Chromosome Location	chr2:111601942-111601943
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111596367..111598097-chr2:111601001..111603633,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10179923	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]
rs10180020	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12476878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12711785	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13019266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1533295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1533298	0.95[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1533300	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1554006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1969232	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1969233	0.80[EUR][1000 genomes]
rs2341873	0.82[CEU][hapmap]
rs2612698	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs2612700	0.87[CEU][hapmap]
rs4848317	0.83[CEU][hapmap]
rs4849134	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849135	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4849155	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs66782223	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7576541	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7588925	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9917154	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111562800-111604000	Weak transcription	Lung	lung
2	chr2:111596400-111603400	Weak transcription	Fetal Brain Male	brain
3	chr2:111596400-111611600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:111596800-111609600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:111597000-111611400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:111597200-111604000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:111597600-111604000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:111598600-111604000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:111599000-111606800	Enhancers	Fetal Thymus	thymus
10	chr2:111599600-111602200	Enhancers	Dnd41	blood
11	chr2:111600800-111602000	Enhancers	Primary T cells from cord blood	blood
12	chr2:111600800-111602200	Enhancers	Fetal Muscle Leg	muscle
13	chr2:111600800-111602600	Enhancers	GM12878-XiMat	blood
14	chr2:111600800-111607600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:111601000-111602000	Enhancers	Fetal Lung	lung
16	chr2:111601400-111603400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:111601400-111604000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:111601400-111604000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:111601400-111604800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:111601400-111611000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:111601600-111602000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:111601600-111602200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr2:111601600-111603600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:111601600-111604000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:111601600-111604200	Weak transcription	Primary B cells from cord blood	blood
26	chr2:111601600-111609200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:111601800-111603600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:111601800-111603600	Weak transcription	Thymus	Thymus
29	chr2:111601800-111603800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:111601800-111606000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:111601800-111609400	Weak transcription	Spleen	Spleen
32	chr2:111601800-111611600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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