Variant report

Variant	rs11799741
Chromosome Location	chr1:168659446-168659447
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	chr1:168658040..168660028-chr1:169075019..169076893,2	MCF-7	breast:
2	chr1:168408540..168410593-chr1:168659202..168660877,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10489358	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489359	0.81[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10918958	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108637	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588432	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11588434	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11590795	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12094644	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726636	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12727749	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12745063	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12748015	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12749426	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12749876	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1337747	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1337748	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1412334	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1412335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415678	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1415680	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16861287	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502304	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17502351	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17502574	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17561671	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2223911	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2419126	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2419128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34099957	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35492795	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4437856	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58620990	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688592	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs726055	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7416358	0.93[AMR][1000 genomes];0.99[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	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv831836	chr1:168538779-168716956	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1001684	chr1:168636622-168663398	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv525556	chr1:168653857-168662352	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11799741	SELL	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168655200-168659600	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr1:168656200-168660800	Enhancers	Colon Smooth Muscle	Colon
3	chr1:168657000-168661000	Enhancers	Rectal Smooth Muscle	rectum
4	chr1:168657200-168660600	Enhancers	Fetal Heart	heart
5	chr1:168657600-168659600	Enhancers	Ovary	ovary
6	chr1:168657800-168660000	Enhancers	A549	lung
7	chr1:168657800-168660400	Enhancers	Fetal Intestine Small	intestine
8	chr1:168658000-168660000	Enhancers	Fetal Intestine Large	intestine
9	chr1:168658000-168660000	Enhancers	Fetal Stomach	stomach
10	chr1:168658000-168660600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:168658000-168662000	Enhancers	Pancreas	Pancrea
12	chr1:168658200-168662000	Weak transcription	Fetal Kidney	kidney
13	chr1:168658200-168662400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:168658200-168662800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:168658200-168663200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:168658400-168661000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:168658600-168659600	Enhancers	Gastric	stomach
18	chr1:168658600-168659600	Enhancers	Right Ventricle	heart
19	chr1:168658800-168659600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:168658800-168659600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:168658800-168659600	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr1:168658800-168660000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:168658800-168660000	Flanking Active TSS	HepG2	liver
24	chr1:168659000-168659800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:168659000-168660000	Enhancers	HMEC	breast
26	chr1:168659000-168660200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:168659200-168659600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:168659200-168660200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:168659400-168659800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:168659400-168660000	Enhancers	HSMM	muscle
31	chr1:168659400-168660000	Enhancers	NH-A	brain
32	chr1:168659400-168662800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:168659400-168662800	Weak transcription	Stomach Mucosa	stomach
34	chr1:168659400-168669400	Weak transcription	Small Intestine	intestine

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