Variant report

Variant	rs272500
Chromosome Location	chr1:86827633-86827634
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	chr1:86823768..86826042-chr1:86827235..86830172,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10493790	0.92[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11161810	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11161812	0.96[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11161814	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11161816	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs11161817	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11161831	0.83[CEU][hapmap]
rs1158833	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1182098	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1182099	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1182101	0.85[EUR][1000 genomes]
rs12119411	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12123660	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12125965	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12130284	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12145243	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12146009	0.81[CEU][hapmap]
rs12403033	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12406320	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1413431	0.92[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1413432	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17409213	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17409304	0.92[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17449526	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1931360	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1931361	0.84[EUR][1000 genomes]
rs1931362	0.84[EUR][1000 genomes]
rs272489	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs272493	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs272495	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs272496	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs272497	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs272499	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs272501	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs272505	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs272509	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs272512	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs272514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs272515	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs272518	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35489949	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3737673	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3765983	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs421105	0.91[ASW][hapmap];1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs423991	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5026277	0.96[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs56104000	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56408800	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57210989	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61124915	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs977919	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs272500	CLCA4	cis	cerebellum	SCAN
rs272500	ODF2L	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86808600-86842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:86813800-86836400	Weak transcription	Lung	lung
3	chr1:86813800-86842600	Weak transcription	Fetal Heart	heart
4	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
5	chr1:86816000-86842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:86817200-86843800	Weak transcription	Small Intestine	intestine
7	chr1:86817600-86843000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:86817800-86828000	Weak transcription	Fetal Stomach	stomach
9	chr1:86817800-86828000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:86817800-86835400	Weak transcription	Esophagus	oesophagus
11	chr1:86817800-86840000	Weak transcription	GM12878-XiMat	blood
12	chr1:86817800-86842400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:86818000-86842600	Weak transcription	Fetal Intestine Small	intestine
14	chr1:86818000-86843200	Weak transcription	Pancreas	Pancrea
15	chr1:86818000-86851600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:86818200-86841000	Weak transcription	Fetal Kidney	kidney
17	chr1:86819000-86838400	Weak transcription	NHDF-Ad	bronchial
18	chr1:86819800-86828000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:86819800-86830200	Weak transcription	Spleen	Spleen
20	chr1:86819800-86839400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:86819800-86839400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:86819800-86840200	Weak transcription	Brain Angular Gyrus	brain
23	chr1:86819800-86840200	Weak transcription	HMEC	breast
24	chr1:86819800-86842200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:86819800-86842600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:86819800-86843000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:86819800-86843000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:86820200-86840200	Weak transcription	Brain Anterior Caudate	brain
29	chr1:86820200-86841200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:86820200-86842600	Weak transcription	Brain Germinal Matrix	brain
31	chr1:86820200-86843400	Weak transcription	Left Ventricle	heart
32	chr1:86820200-86854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:86820200-86854800	Weak transcription	HSMMtube	muscle
34	chr1:86820400-86835000	Weak transcription	HSMM	muscle
35	chr1:86820400-86838400	Weak transcription	Primary B cells from cord blood	blood
36	chr1:86820400-86838400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:86820400-86838400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:86820400-86838600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:86820400-86839400	Weak transcription	NH-A	brain
40	chr1:86820400-86842400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:86820400-86842800	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:86820400-86842800	Weak transcription	Placenta	Placenta
43	chr1:86820400-86845400	Weak transcription	Hela-S3	cervix
44	chr1:86820400-86846200	Weak transcription	NHLF	lung
45	chr1:86820400-86846400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:86820400-86847000	Weak transcription	Liver	Liver
47	chr1:86820400-86848000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:86820400-86860200	Weak transcription	NHEK	skin
49	chr1:86820600-86838400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:86820600-86839400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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