Variant report

Variant	rs6590949
Chromosome Location	chr11:102011954-102011955
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	chr11:102010849..102012537-chr11:102015690..102017835,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10750632	0.81[EUR][1000 genomes]
rs10750633	0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10750634	0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10791564	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10791565	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895256	0.82[MEX][hapmap]
rs10895258	0.82[EUR][1000 genomes]
rs10895259	0.82[EUR][1000 genomes]
rs10895261	0.82[EUR][1000 genomes]
rs10895262	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10895263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10895264	0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10895265	0.80[ASN][1000 genomes]
rs10895266	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11225134	0.82[EUR][1000 genomes]
rs11225135	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs11225139	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11225141	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11225146	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11225147	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11225149	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11225151	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11603468	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11606471	0.81[EUR][1000 genomes]
rs11607135	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12223094	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12796162	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1365330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1426392	0.87[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1426394	0.82[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1426398	0.80[MKK][hapmap]
rs1834595	0.82[EUR][1000 genomes]
rs1834596	0.87[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1893497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1895917	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1942688	0.82[EUR][1000 genomes]
rs1942689	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs1942690	0.82[EUR][1000 genomes]
rs1942691	0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs2003357	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2019070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3890538	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4329661	0.83[EUR][1000 genomes]
rs4442513	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4754833	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4754834	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60304309	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61538959	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7106388	0.82[MEX][hapmap]
rs7108698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7108820	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7117239	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7123862	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7124280	0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7126535	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7127597	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7130772	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7483889	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7924449	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7924737	0.82[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7927957	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7928547	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs7938172	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs948737	0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs9787890	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3362945	chr11:101736547-102114246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv898333	chr11:101832670-102079986	Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1052348	chr11:101987090-102255753	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv556141	chr11:101988061-102207851	Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1050961	chr11:101993880-102253717	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1051735	chr11:101993880-102255753	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv530646	chr11:102000840-102238992	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6590949	CASP1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101983600-102014800	Weak transcription	Pancreas	Pancrea
2	chr11:101989600-102015200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:101991600-102012400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:101991600-102015200	Weak transcription	Fetal Kidney	kidney
5	chr11:101991600-102015600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:101998600-102033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:101998600-102034200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:101998800-102014400	Weak transcription	Liver	Liver
9	chr11:101998800-102014600	Weak transcription	Small Intestine	intestine
10	chr11:101998800-102014800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr11:101999000-102012600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:102000800-102034000	Weak transcription	Lung	lung
13	chr11:102004600-102015600	Weak transcription	Ovary	ovary
14	chr11:102005800-102033000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:102006200-102014600	Weak transcription	Fetal Stomach	stomach
16	chr11:102006400-102012000	Weak transcription	Psoas Muscle	Psoas
17	chr11:102006400-102015400	Weak transcription	Right Atrium	heart
18	chr11:102006400-102015600	Weak transcription	Right Ventricle	heart
19	chr11:102007600-102012000	Weak transcription	Fetal Muscle Leg	muscle
20	chr11:102008800-102012000	Enhancers	HepG2	liver
21	chr11:102008800-102012000	Enhancers	HMEC	breast
22	chr11:102009200-102013200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:102009200-102015200	Weak transcription	Fetal Intestine Small	intestine
24	chr11:102009200-102015600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:102009200-102015600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:102010000-102015600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:102010000-102015600	Weak transcription	HUVEC	blood vessel
28	chr11:102010200-102015200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:102010200-102032400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:102010400-102012000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:102010400-102012000	Weak transcription	Adipose Nuclei	Adipose
32	chr11:102010400-102012800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr11:102010400-102014200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr11:102010400-102014600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:102010400-102014600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr11:102010400-102014600	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:102010400-102014800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:102010400-102015000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr11:102010400-102015600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr11:102010400-102015600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr11:102010400-102015600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr11:102010400-102020800	Weak transcription	Left Ventricle	heart
43	chr11:102010400-102023000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:102010400-102039000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:102010600-102012000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr11:102010600-102012200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:102010600-102013800	Enhancers	NHDF-Ad	bronchial
48	chr11:102010600-102014200	Weak transcription	Stomach Mucosa	stomach
49	chr11:102010600-102014400	Weak transcription	A549	lung
50	chr11:102010600-102015200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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