Variant report

Variant	rs10838425
Chromosome Location	chr11:45169347-45169348
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:70747303..70749893-chr11:45167896..45169684,2	MCF-7	breast:
2	chr11:45167893..45171206-chr11:45200303..45204446,5	MCF-7	breast:
3	chr11:45164160..45171283-chr11:45198764..45207868,26	MCF-7	breast:
4	chr11:45167440..45169930-chr11:45202656..45204248,2	K562	blood:

Variant related genes	Relation type
ENSG00000019485	Chromatin interaction
ENSG00000198954	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10742737	0.84[CEU][hapmap]
rs10742743	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10742744	0.81[JPT][hapmap]
rs10742745	0.82[JPT][hapmap]
rs1078930	0.82[JPT][hapmap]
rs11038305	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs11038306	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs12281438	0.86[JPT][hapmap]
rs1487720	0.86[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap]
rs2863159	0.82[JPT][hapmap]
rs3758728	0.82[JPT][hapmap]
rs3781706	0.82[JPT][hapmap]
rs4495881	0.94[EUR][1000 genomes]
rs4755953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6485592	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6485594	0.84[JPT][hapmap]
rs6485595	0.86[JPT][hapmap]
rs6485596	0.85[JPT][hapmap]
rs6485597	0.86[JPT][hapmap]
rs6485598	0.86[JPT][hapmap]
rs7107896	0.86[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs7124466	0.85[CEU][hapmap]
rs7929875	0.86[CEU][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs9667741	0.92[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	nsv825852	chr11:45141386-45228580	Bivalent/Poised TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv541025	chr11:45154352-45193352	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv1048493	chr11:45166054-45205695	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	esv3402611	chr11:45166876-45169824	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	esv3341652	chr11:45167401-45170149	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10838425	GYLTL1B	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45166800-45169600	Active TSS	H9 Cell Line	embryonic stem cell
2	chr11:45167200-45169600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:45167200-45169800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr11:45167200-45170000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr11:45167400-45169600	Active TSS	Psoas Muscle	Psoas
6	chr11:45167400-45169600	Active TSS	Right Atrium	heart
7	chr11:45167400-45169800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:45167400-45169800	Active TSS	HSMM	muscle
9	chr11:45167400-45170000	Active TSS	A549	lung
10	chr11:45167600-45169400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:45167600-45169400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:45167600-45169400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:45167600-45169400	Active TSS	Esophagus	oesophagus
14	chr11:45167600-45169400	Active TSS	Left Ventricle	heart
15	chr11:45167600-45169400	Active TSS	Right Ventricle	heart
16	chr11:45167600-45169400	Active TSS	NHLF	lung
17	chr11:45167600-45169600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr11:45167600-45169600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:45167600-45169600	Active TSS	Aorta	Aorta
20	chr11:45167600-45169600	Active TSS	Fetal Intestine Large	intestine
21	chr11:45167600-45169600	Active TSS	Ovary	ovary
22	chr11:45167600-45169800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:45167600-45169800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:45167800-45169400	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr11:45167800-45169400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:45167800-45169400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:45167800-45169400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr11:45167800-45169400	Active TSS	Fetal Brain Female	brain
29	chr11:45167800-45169400	Active TSS	Pancreas	Pancrea
30	chr11:45167800-45169400	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr11:45167800-45169400	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr11:45167800-45169600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:45167800-45169600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:45167800-45169600	Active TSS	Small Intestine	intestine
35	chr11:45167800-45169800	Active TSS	NHDF-Ad	bronchial
36	chr11:45168000-45169400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr11:45168000-45169400	Active TSS	Gastric	stomach
38	chr11:45168000-45169400	Active TSS	Lung	lung
39	chr11:45168200-45169400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr11:45168800-45169400	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr11:45168800-45169400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:45168800-45169600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr11:45168800-45169800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr11:45169000-45169400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:45169000-45169400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr11:45169000-45169400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:45169000-45169400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:45169000-45169400	ZNF genes & repeats	Fetal Brain Male	brain
49	chr11:45169000-45169400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
50	chr11:45169000-45169400	Flanking Active TSS	K562	blood

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