Variant report

Variant	rs11634828
Chromosome Location	chr15:75919195-75919196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:75919138-75919370	K562	blood:	n/a	chr15:75919151-75919168 chr15:75919154-75919167
2	POLR2A	chr15:75917595-75919228	PANC-1	pancreas:	n/a	n/a
3	MAX	chr15:75917312-75919280	A549	lung:	n/a	chr15:75919196-75919205
4	SIX5	chr15:75917597-75919261	A549	lung:	n/a	n/a
5	POLR2A	chr15:75917273-75919214	PANC-1	pancreas:	n/a	n/a
6	CEBPB	chr15:75918802-75919399	K562	blood:	n/a	chr15:75919151-75919168 chr15:75919154-75919167
7	RCOR1	chr15:75917767-75919235	K562	blood:	n/a	n/a
8	HCFC1	chr15:75917329-75919373	Hela-S3	cervix:	n/a	n/a
9	FOSL2	chr15:75917518-75919242	A549	lung:	n/a	chr15:75918346-75918355
10	CEBPB	chr15:75918965-75919465	K562	blood:	n/a	chr15:75919151-75919168 chr15:75919154-75919167
11	RAD21	chr15:75917324-75919271	SK-N-SH	brain:	n/a	chr15:75918093-75918107 chr15:75918092-75918106 chr15:75918089-75918102 chr15:75918090-75918100
12	ZNF384	chr15:75917955-75919451	K562	blood:	n/a	n/a
13	RCOR1	chr15:75917343-75919204	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75659095..75662742-chr15:75916445..75919940,7	K562	blood:
2	chr15:75916258..75921824-chr15:75930808..75933710,8	MCF-7	breast:
3	chr15:75743503..75749103-chr15:75916446..75919686,11	K562	blood:
4	chr15:75916634..75921269-chr15:75928640..75933625,8	MCF-7	breast:
5	chr15:75655021..75659066-chr15:75918154..75920170,3	K562	blood:
6	chr15:75743363..75745017-chr15:75917841..75919520,2	K562	blood:
7	chr15:75745526..75749103-chr15:75915153..75919928,6	K562	blood:
8	chr15:75652075..75654560-chr15:75917811..75919944,2	K562	blood:

Variant related genes	Relation type
SNUPN	TF binding region
ENSG00000177971	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000169375	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11547316	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11632887	1.00[CHD][hapmap]
rs11635996	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes]
rs11638663	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
6	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
7	nsv531902	chr15:75724505-75919237	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11634828	MAN2C1	cis	parietal	SCAN
rs11634828	MAN2C1	cis	Thyroid	GTEx
rs11634828	MAN2C1	cis	Whole Blood	GTEx
rs11634828	MAN2C1	cis	cerebellum	SCAN
rs11634828	SNX33	cis	cerebellum	SCAN
rs11634828	MAN2C1	cis	lung	GTEx
rs11634828	SNUPN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75916800-75919200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:75917000-75919200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr15:75918200-75919200	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr15:75918200-75919400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr15:75918200-75919800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr15:75918400-75919200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:75918400-75919200	Flanking Active TSS	Liver	Liver
8	chr15:75918400-75919200	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr15:75918400-75919200	Flanking Active TSS	GM12878-XiMat	blood
10	chr15:75918400-75919200	Flanking Active TSS	Hela-S3	cervix
11	chr15:75918400-75919200	Flanking Active TSS	K562	blood
12	chr15:75918600-75919200	Flanking Active TSS	Fetal Lung	lung
13	chr15:75918600-75919200	Flanking Active TSS	Dnd41	blood
14	chr15:75918600-75919200	Enhancers	NHLF	lung
15	chr15:75918600-75931000	Weak transcription	Aorta	Aorta
16	chr15:75918800-75919200	Enhancers	Primary B cells from peripheral blood	blood
17	chr15:75918800-75919200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:75918800-75919200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr15:75918800-75919200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:75918800-75919200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr15:75918800-75919200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr15:75918800-75919200	Enhancers	Colon Smooth Muscle	Colon
23	chr15:75918800-75919200	Enhancers	Fetal Heart	heart
24	chr15:75918800-75919200	Enhancers	Fetal Intestine Small	intestine
25	chr15:75918800-75919200	Enhancers	Fetal Muscle Leg	muscle
26	chr15:75918800-75919200	Enhancers	Placenta	Placenta
27	chr15:75918800-75919200	Flanking Active TSS	HepG2	liver
28	chr15:75918800-75919200	Active TSS	NH-A	brain
29	chr15:75918800-75919200	Enhancers	NHDF-Ad	bronchial
30	chr15:75918800-75919800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:75918800-75919800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:75918800-75919800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:75918800-75919800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:75918800-75919800	Weak transcription	Lung	lung
35	chr15:75918800-75919800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr15:75918800-75920000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:75918800-75920000	Weak transcription	Pancreas	Pancrea
38	chr15:75918800-75920200	Enhancers	Primary hematopoietic stem cells	blood
39	chr15:75918800-75920200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:75918800-75920400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:75918800-75920600	Enhancers	HMEC	breast
42	chr15:75918800-75921000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:75918800-75926800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:75918800-75929200	Weak transcription	Brain Germinal Matrix	brain
45	chr15:75918800-75929400	Weak transcription	Psoas Muscle	Psoas
46	chr15:75918800-75929600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr15:75918800-75929600	Weak transcription	Brain Angular Gyrus	brain
48	chr15:75918800-75929600	Weak transcription	Brain Anterior Caudate	brain
49	chr15:75918800-75929600	Weak transcription	Spleen	Spleen
50	chr15:75918800-75929600	Weak transcription	HSMM	muscle

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