Variant report

Variant	rs2561524
Chromosome Location	chr5:100164992-100164993
allele	A/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: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10515265	1.00[EUR][1000 genomes]
rs10515266	1.00[EUR][1000 genomes]
rs1423381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[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[JPT][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]
rs17160844	1.00[CEU][hapmap];0.94[AMR][1000 genomes]
rs17161136	0.87[AMR][1000 genomes]
rs2544911	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]
rs2544912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544914	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]
rs2544915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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[JPT][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];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]
rs2561525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561527	0.84[AFR][1000 genomes];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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3776165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[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];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:54 , 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	chr5:100161200-100165000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:100161200-100165000	Enhancers	HSMM	muscle
8	chr5:100161600-100165000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:100161800-100165200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr5:100162000-100165200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:100162200-100165000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:100162800-100165000	Flanking Active TSS	GM12878-XiMat	blood
13	chr5:100163000-100165000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:100163000-100165000	Enhancers	Brain Germinal Matrix	brain
15	chr5:100163000-100165000	Enhancers	Placenta Amnion	Placenta Amnion
16	chr5:100163000-100165000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr5:100163000-100165000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr5:100163000-100165000	Enhancers	HUVEC	blood vessel
19	chr5:100163000-100165000	Enhancers	NHEK	skin
20	chr5:100163200-100165000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr5:100163200-100165000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr5:100163200-100165000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr5:100163200-100165000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:100163400-100165000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr5:100163400-100165000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr5:100163400-100165000	Enhancers	Left Ventricle	heart
27	chr5:100163800-100165000	Enhancers	Primary T cells fromperipheralblood	blood
28	chr5:100164000-100165800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:100164000-100173800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:100164200-100165000	Enhancers	H9 Cell Line	embryonic stem cell
31	chr5:100164200-100165000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr5:100164200-100165000	Enhancers	Brain Substantia Nigra	brain
33	chr5:100164200-100165000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr5:100164200-100171800	Weak transcription	Fetal Stomach	stomach
35	chr5:100164200-100174800	Weak transcription	Placenta	Placenta
36	chr5:100164200-100176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:100164400-100165000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:100164400-100165000	Strong transcription	Primary T cells from cord blood	blood
39	chr5:100164400-100165000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr5:100164400-100170200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:100164400-100173600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr5:100164400-100175000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:100164400-100175800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr5:100164600-100165000	Enhancers	Brain Cingulate Gyrus	brain
45	chr5:100164600-100168400	Weak transcription	Primary B cells from cord blood	blood
46	chr5:100164600-100174800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:100164600-100175000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr5:100164800-100165000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:100164800-100165000	Enhancers	Spleen	Spleen
50	chr5:100164800-100165200	Enhancers	Monocytes-CD14+_RO01746	blood

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