Variant report

Variant	rs6700502
Chromosome Location	chr1:45513072-45513073
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	chr1:45503364..45509535-chr1:45510898..45517046,6	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11211075	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11211077	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11211080	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1143726	1.00[CEU][hapmap];0.89[YRI][hapmap];0.93[EUR][1000 genomes]
rs1143727	0.96[EUR][1000 genomes]
rs1144866	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1144867	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1144870	0.89[YRI][hapmap];0.96[EUR][1000 genomes]
rs1144871	1.00[CEU][hapmap];0.89[YRI][hapmap];0.96[EUR][1000 genomes]
rs1152017	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1152018	0.83[CEU][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1152020	0.96[EUR][1000 genomes]
rs1152022	0.96[EUR][1000 genomes]
rs11585488	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs11588448	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12061569	0.82[YRI][hapmap]
rs12086670	0.82[YRI][hapmap]
rs1226722	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1226723	0.93[CEU][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1226727	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1226728	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1226736	0.90[EUR][1000 genomes]
rs1226740	0.90[EUR][1000 genomes]
rs1226749	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes]
rs1226912	0.90[EUR][1000 genomes]
rs12750360	0.96[EUR][1000 genomes]
rs16832411	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1698295	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes]
rs1938302	1.00[CEU][hapmap];0.88[YRI][hapmap];0.90[EUR][1000 genomes]
rs1938406	0.90[EUR][1000 genomes]
rs2211644	0.88[EUR][1000 genomes]
rs2356304	0.87[EUR][1000 genomes]
rs2883902	0.90[EUR][1000 genomes]
rs2997400	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes]
rs2997462	0.88[EUR][1000 genomes]
rs3009973	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes]
rs3009976	0.90[EUR][1000 genomes]
rs3009978	0.90[EUR][1000 genomes]
rs3121731	0.88[EUR][1000 genomes]
rs3121770	0.88[EUR][1000 genomes]
rs3128437	0.88[EUR][1000 genomes]
rs3128443	0.88[EUR][1000 genomes]
rs6429555	0.81[YRI][hapmap]
rs6429558	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6698681	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6702389	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs68139854	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7517524	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7528468	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7548075	0.96[EUR][1000 genomes]
rs7552211	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.99[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:42 , 50 per page) page: 1

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	chr1:45491800-45516400	Weak transcription	Spleen	Spleen
5	chr1:45497400-45525400	Weak transcription	Gastric	stomach
6	chr1:45498000-45525600	Weak transcription	Pancreas	Pancrea
7	chr1:45499200-45516200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:45500400-45516600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:45501400-45516600	Weak transcription	Small Intestine	intestine
10	chr1:45501800-45516200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:45501800-45521200	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:45501800-45527000	Weak transcription	Fetal Brain Male	brain
13	chr1:45502000-45523800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:45502400-45523000	Weak transcription	Aorta	Aorta
15	chr1:45504200-45524200	Weak transcription	Esophagus	oesophagus
16	chr1:45504400-45524000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:45504800-45516400	Weak transcription	Fetal Intestine Large	intestine
18	chr1:45505000-45526000	Weak transcription	Fetal Stomach	stomach
19	chr1:45505200-45514600	Weak transcription	Fetal Intestine Small	intestine
20	chr1:45507600-45527000	Weak transcription	Fetal Kidney	kidney
21	chr1:45508800-45516200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:45509000-45523000	Weak transcription	Brain Angular Gyrus	brain
23	chr1:45509000-45523800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:45509000-45524000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:45509200-45515400	Weak transcription	Brain Substantia Nigra	brain
26	chr1:45509200-45521000	Weak transcription	Brain Anterior Caudate	brain
27	chr1:45509200-45522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:45509400-45513200	Weak transcription	Fetal Brain Female	brain
29	chr1:45509600-45514400	Weak transcription	HepG2	liver
30	chr1:45509600-45516200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:45509600-45516400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:45509600-45522400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:45509600-45526200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:45510000-45516000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:45511200-45521400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:45511400-45513600	Strong transcription	Ovary	ovary
37	chr1:45511400-45521400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:45512000-45514800	Weak transcription	Brain Germinal Matrix	brain
39	chr1:45512200-45513600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr1:45512400-45523800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:45512800-45513600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:45512800-45513600	Enhancers	Skeletal Muscle Female	skeletal muscle

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