Variant report

Variant	rs575008
Chromosome Location	chr11:107707896-107707897
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:107705879..107708165-chr11:107709790..107712179,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10890766	0.80[ASN][1000 genomes]
rs2442683	1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2442684	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2456080	0.92[EUR][1000 genomes]
rs3105397	0.84[AMR][1000 genomes]
rs3105399	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs480641	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs483463	0.82[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs483874	0.90[JPT][hapmap]
rs488030	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs488081	0.82[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs488512	1.00[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs493037	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs502253	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs502398	0.81[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs523750	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs542931	0.85[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs543568	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs564569	0.82[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs565438	0.82[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs566238	0.82[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs573074	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs578300	0.83[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs587130	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs651531	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs657608	0.82[EUR][1000 genomes]
rs660042	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs668785	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs676108	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1039425	chr11:107468681-107895836	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv427899	chr11:107471544-107805894	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049524	chr11:107540937-107954011	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1038581	chr11:107564274-107838386	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv898378	chr11:107580985-107847983	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv521771	chr11:107590335-107904646	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1048938	chr11:107604473-107929950	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1035229	chr11:107653731-107717190	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv1052829	chr11:107686808-107725297	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv1045388	chr11:107686808-107733498	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	esv3417743	chr11:107699670-107725103	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs575008	SLN	cis	parietal	SCAN
rs575008	FDX1	cis	parietal	SCAN
rs575008	SLC35F2	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107673400-107727800	Weak transcription	Primary B cells from cord blood	blood
2	chr11:107691200-107709600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:107696600-107711000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr11:107697200-107709800	Weak transcription	GM12878-XiMat	blood
5	chr11:107702200-107709800	Weak transcription	A549	lung
6	chr11:107702200-107710600	Weak transcription	Stomach Mucosa	stomach
7	chr11:107702400-107710600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:107702400-107710800	Weak transcription	Gastric	stomach
9	chr11:107702800-107710600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr11:107703000-107708800	Weak transcription	HUVEC	blood vessel
11	chr11:107703600-107709800	Weak transcription	K562	blood
12	chr11:107703600-107710400	Weak transcription	Esophagus	oesophagus
13	chr11:107703800-107709800	Weak transcription	HMEC	breast
14	chr11:107704200-107710000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:107704400-107709800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:107705000-107710800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:107705200-107718600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:107706000-107710600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr11:107706200-107710600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr11:107706600-107709400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:107706600-107711000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:107706800-107711000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:107706800-107711400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr11:107707200-107708000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:107707200-107708200	Enhancers	Duodenum Mucosa	Duodenum
26	chr11:107707200-107710600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:107707400-107708200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr11:107707400-107710600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:107707400-107711000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr11:107707400-107711000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:107707600-107708200	Weak transcription	Fetal Brain Male	brain
32	chr11:107707600-107711000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:107707600-107711600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:107707800-107708000	Genic enhancers	NHEK	skin
35	chr11:107707800-107709800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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