Variant report

Variant	rs1554006
Chromosome Location	chr2:111604113-111604114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111603779..111605764-chr2:111610713..111613145,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10179923	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]
rs10180020	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[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]
rs10180446	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]
rs12476878	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12711785	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13019266	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1533295	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1533298	1.00[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1533300	0.91[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1969232	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2612700	0.81[CEU][hapmap]
rs4849134	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4849135	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66782223	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7576541	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7588925	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[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]
rs9917154	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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:42 , 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	chr2:111596800-111609600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:111597000-111611400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr2:111599000-111606800	Enhancers	Fetal Thymus	thymus
5	chr2:111600800-111607600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:111601400-111604800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:111601400-111611000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:111601600-111604200	Weak transcription	Primary B cells from cord blood	blood
9	chr2:111601600-111609200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:111601800-111606000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:111601800-111609400	Weak transcription	Spleen	Spleen
12	chr2:111601800-111611600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:111602000-111604200	Weak transcription	Fetal Lung	lung
14	chr2:111603200-111605800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr2:111603200-111607000	Enhancers	Primary T cells from cord blood	blood
16	chr2:111603400-111604200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr2:111603400-111604600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr2:111603400-111606200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:111603400-111606400	Enhancers	Fetal Brain Male	brain
20	chr2:111603400-111606600	Enhancers	Primary T cells fromperipheralblood	blood
21	chr2:111603400-111606800	Enhancers	Dnd41	blood
22	chr2:111603600-111604600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr2:111603600-111606800	Enhancers	Thymus	Thymus
24	chr2:111603800-111605000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:111603800-111605000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:111603800-111605600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:111603800-111605800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:111603800-111606000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr2:111603800-111606200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr2:111604000-111604200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr2:111604000-111604200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr2:111604000-111604200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:111604000-111604200	Enhancers	Fetal Brain Female	brain
34	chr2:111604000-111604200	Enhancers	Lung	lung
35	chr2:111604000-111605000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr2:111604000-111605000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:111604000-111605000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:111604000-111605400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:111604000-111605400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:111604000-111605800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:111604000-111606400	Enhancers	GM12878-XiMat	blood
42	chr2:111604000-111611600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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