Variant report

Variant	rs7517524
Chromosome Location	chr1:45516522-45516523
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45503364..45509535-chr1:45510898..45517046,6	K562	blood:
2	chr1:45492852..45494427-chr1:45515259..45518004,2	K562	blood:
3	chr1:45477633..45480305-chr1:45514821..45518438,3	K562	blood:

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11211075	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211077	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211080	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1143726	1.00[CEU][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1143727	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1144866	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1144867	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1144870	0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1144871	1.00[CEU][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1152017	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1152018	0.83[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1152020	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1152022	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11585488	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs11588448	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12061569	0.85[YRI][hapmap]
rs12086670	0.85[YRI][hapmap]
rs1226722	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1226723	0.93[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1226727	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1226728	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1226736	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1226740	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1226749	1.00[CEU][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1226911	0.81[AMR][1000 genomes]
rs1226912	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12750360	0.97[EUR][1000 genomes]
rs16832411	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1698295	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1938302	1.00[CEU][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1938406	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2211644	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2356304	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2883902	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2997400	1.00[CEU][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2997462	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3009973	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3009976	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3009978	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3121731	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3121770	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3128437	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3128443	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6429555	0.85[YRI][hapmap]
rs6429558	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6698681	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6700502	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6702389	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs68139854	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7528468	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7548075	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7552211	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45481200-45525000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:45481200-45527400	Weak transcription	Left Ventricle	heart
3	chr1:45482000-45523800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:45497400-45525400	Weak transcription	Gastric	stomach
5	chr1:45498000-45525600	Weak transcription	Pancreas	Pancrea
6	chr1:45500400-45516600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:45501400-45516600	Weak transcription	Small Intestine	intestine
8	chr1:45501800-45521200	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:45501800-45527000	Weak transcription	Fetal Brain Male	brain
10	chr1:45502000-45523800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:45502400-45523000	Weak transcription	Aorta	Aorta
12	chr1:45504200-45524200	Weak transcription	Esophagus	oesophagus
13	chr1:45504400-45524000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:45505000-45526000	Weak transcription	Fetal Stomach	stomach
15	chr1:45507600-45527000	Weak transcription	Fetal Kidney	kidney
16	chr1:45509000-45523000	Weak transcription	Brain Angular Gyrus	brain
17	chr1:45509000-45523800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:45509000-45524000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:45509200-45521000	Weak transcription	Brain Anterior Caudate	brain
20	chr1:45509200-45522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:45509600-45522400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:45509600-45526200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:45511200-45521400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:45511400-45521400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:45512400-45523800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:45513200-45517400	Strong transcription	Fetal Brain Female	brain
27	chr1:45513600-45519600	Weak transcription	Ovary	ovary
28	chr1:45513600-45525400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:45513600-45526200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:45514400-45519200	Strong transcription	HepG2	liver
31	chr1:45514800-45517200	Strong transcription	Brain Germinal Matrix	brain
32	chr1:45515400-45516600	Enhancers	Primary T cells from cord blood	blood
33	chr1:45515600-45517000	Weak transcription	Brain Substantia Nigra	brain
34	chr1:45515800-45516600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr1:45516000-45516600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr1:45516200-45516600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr1:45516200-45516600	Enhancers	Dnd41	blood
38	chr1:45516200-45517000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:45516200-45517400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:45516400-45516600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr1:45516400-45516600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:45516400-45516600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr1:45516400-45516600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:45516400-45516600	Enhancers	Duodenum Mucosa	Duodenum
45	chr1:45516400-45516800	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr1:45516400-45516800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr1:45516400-45516800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:45516400-45517000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr1:45516400-45517000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr1:45516400-45517000	Enhancers	Thymus	Thymus

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