Variant report

Variant	rs2544911
Chromosome Location	chr5:100164220-100164221
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	chr5:100157247..100161325-chr5:100161571..100164994,4	MCF-7	breast:
2	chr5:100163874..100166036-chr5:100222843..100225362,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10515265	1.00[EUR][1000 genomes]
rs10515266	1.00[EUR][1000 genomes]
rs1423381	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159344	1.00[EUR][1000 genomes]
rs17159370	1.00[EUR][1000 genomes]
rs17159464	1.00[EUR][1000 genomes]
rs17159467	1.00[EUR][1000 genomes]
rs17159519	1.00[EUR][1000 genomes]
rs17159602	1.00[EUR][1000 genomes]
rs17159616	1.00[EUR][1000 genomes]
rs17159626	1.00[EUR][1000 genomes]
rs17160705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17160732	1.00[CEU][hapmap];0.98[AMR][1000 genomes]
rs17160771	1.00[GIH][hapmap];0.85[MEX][hapmap]
rs17160844	1.00[CEU][hapmap];0.89[MEX][hapmap];0.94[AMR][1000 genomes]
rs17161136	0.87[AMR][1000 genomes]
rs2544912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2544914	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544916	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2544917	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2544919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2548275	0.88[AMR][1000 genomes]
rs2548277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561527	0.82[AMR][1000 genomes]
rs2725118	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2725123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3776165	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776166	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776172	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs3776173	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs3776179	0.84[ASN][1000 genomes]
rs3857364	1.00[EUR][1000 genomes]
rs6595534	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes]
rs6897681	1.00[EUR][1000 genomes]
rs73162282	0.84[ASN][1000 genomes]
rs73775624	1.00[EUR][1000 genomes]
rs768777	1.00[EUR][1000 genomes]
rs980901	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	esv1834675	chr5:100143084-100535029	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100147600-100218000	Weak transcription	Thymus	Thymus
2	chr5:100147800-100179000	Weak transcription	Fetal Thymus	thymus
3	chr5:100148600-100173200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr5:100159800-100170800	Strong transcription	Dnd41	blood
5	chr5:100161000-100165000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr5:100161200-100164400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:100161200-100165000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:100161200-100165000	Enhancers	HSMM	muscle
9	chr5:100161400-100164400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:100161600-100165000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:100161800-100165200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr5:100162000-100165200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:100162200-100165000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:100162600-100164800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:100162800-100165000	Flanking Active TSS	GM12878-XiMat	blood
16	chr5:100163000-100164400	Genic enhancers	Primary T cells from cord blood	blood
17	chr5:100163000-100164400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:100163000-100164400	Enhancers	HMEC	breast
19	chr5:100163000-100164800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:100163000-100164800	Enhancers	Primary B cells from peripheral blood	blood
21	chr5:100163000-100164800	Enhancers	Adipose Nuclei	Adipose
22	chr5:100163000-100164800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr5:100163000-100165000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:100163000-100165000	Enhancers	Brain Germinal Matrix	brain
25	chr5:100163000-100165000	Enhancers	Placenta Amnion	Placenta Amnion
26	chr5:100163000-100165000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr5:100163000-100165000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr5:100163000-100165000	Enhancers	HUVEC	blood vessel
29	chr5:100163000-100165000	Enhancers	NHEK	skin
30	chr5:100163200-100164400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr5:100163200-100164400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr5:100163200-100164400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr5:100163200-100164400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:100163200-100164400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:100163200-100164400	Enhancers	Brain Angular Gyrus	brain
36	chr5:100163200-100164400	Enhancers	Fetal Brain Female	brain
37	chr5:100163200-100164400	Enhancers	Fetal Lung	lung
38	chr5:100163200-100164400	Enhancers	Fetal Muscle Leg	muscle
39	chr5:100163200-100164400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr5:100163200-100164600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr5:100163200-100164800	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr5:100163200-100164800	Enhancers	HSMMtube	muscle
43	chr5:100163200-100165000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr5:100163200-100165000	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr5:100163200-100165000	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr5:100163200-100165000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:100163400-100164800	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr5:100163400-100164800	Enhancers	Small Intestine	intestine
49	chr5:100163400-100165000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr5:100163400-100165000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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