Variant report

Variant	rs616601
Chromosome Location	chr18:29890042-29890043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29887452..29890348-chr18:30046410..30049276,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10502592	0.88[CHB][hapmap]
rs11876773	0.88[CHB][hapmap]
rs1689030	0.94[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs16963285	0.88[CHB][hapmap]
rs1824304	0.88[CHB][hapmap]
rs594344	0.86[YRI][hapmap]
rs595792	0.94[CEU][hapmap]
rs598074	0.93[EUR][1000 genomes]
rs606638	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs619154	0.86[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs625361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638868	0.85[YRI][hapmap]
rs643836	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs644274	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs668857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671090	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs677721	0.86[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681347	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs686196	0.88[CEU][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];0.83[YRI][hapmap]
rs687850	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7230250	0.88[CHB][hapmap]
rs736218	0.88[CHB][hapmap]
rs8084215	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv833616	chr18:29792336-29964212	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv528846	chr18:29832147-29890042	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv2517711	chr18:29887850-29890139	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv576639	chr18:29888660-29891593	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29868200-29923800	Weak transcription	Gastric	stomach
2	chr18:29878400-29896000	Weak transcription	Brain Anterior Caudate	brain
3	chr18:29878600-29890200	Weak transcription	Brain Angular Gyrus	brain
4	chr18:29880800-29897000	Weak transcription	Lung	lung
5	chr18:29881600-29892200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr18:29883000-29890800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr18:29883000-29891400	Weak transcription	Adipose Nuclei	Adipose
8	chr18:29883000-29891600	Weak transcription	Pancreas	Pancrea
9	chr18:29883000-29895800	Weak transcription	Stomach Mucosa	stomach
10	chr18:29883000-29897000	Weak transcription	Fetal Intestine Small	intestine
11	chr18:29883000-29897000	Weak transcription	Left Ventricle	heart
12	chr18:29883400-29896800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr18:29883800-29893000	Weak transcription	Fetal Heart	heart
14	chr18:29886600-29892000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr18:29887400-29890200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr18:29888000-29891200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr18:29888200-29890400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr18:29888200-29891000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr18:29888600-29890400	Enhancers	NH-A	brain
20	chr18:29888800-29890200	Strong transcription	Liver	Liver
21	chr18:29888800-29890400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr18:29888800-29891000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:29888800-29891000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr18:29888800-29891000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr18:29888800-29891000	Enhancers	Colon Smooth Muscle	Colon
26	chr18:29889000-29890400	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr18:29889000-29891000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr18:29889000-29891000	Enhancers	Ovary	ovary
29	chr18:29889000-29891600	Enhancers	Fetal Muscle Leg	muscle
30	chr18:29889200-29890200	Weak transcription	Brain Substantia Nigra	brain
31	chr18:29889200-29891000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr18:29889200-29891600	Weak transcription	Right Ventricle	heart
33	chr18:29889200-29892400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr18:29889200-29893000	Weak transcription	Small Intestine	intestine
35	chr18:29889200-29896800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr18:29889400-29890200	Enhancers	HSMMtube	muscle
37	chr18:29889400-29890400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr18:29889400-29891200	Enhancers	Rectal Smooth Muscle	rectum
39	chr18:29889400-29891800	Weak transcription	Right Atrium	heart
40	chr18:29889400-29892600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr18:29889400-29895600	Weak transcription	HSMM	muscle
42	chr18:29889400-29895800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr18:29889400-29896200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr18:29889400-29896400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr18:29889400-29896400	Weak transcription	Aorta	Aorta
46	chr18:29889400-29904200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr18:29889600-29891600	Weak transcription	Fetal Intestine Large	intestine
48	chr18:29889600-29895600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr18:29889800-29890400	Enhancers	Brain Cingulate Gyrus	brain
50	chr18:29889800-29890800	Enhancers	Fetal Stomach	stomach

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