Variant report

Variant	rs11169170
Chromosome Location	chr12:50223013-50223014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr12:50221265-50223147	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:50222751-50223128	GM12878	blood:	n/a	n/a
3	MXI1	chr12:50220808-50223273	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr12:50221936-50223089	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:50223011-50223056	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr12:50221883-50223124	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:50220552-50223242	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr12:50221398-50223072	A549	lung:	n/a	n/a
9	TAF7	chr12:50222252-50223047	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAZ	chr12:50220750-50223349	IMR90	lung:	n/a	n/a
11	MXI1	chr12:50221018-50223194	IMR90	lung:	n/a	n/a
12	HCFC1	chr12:50220291-50223515	Hela-S3	cervix:	n/a	n/a
13	CHD1	chr12:50222452-50223042	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr12:50221879-50223023	K562	blood:	n/a	n/a
15	MAX	chr12:50221086-50223054	HepG2	liver:	n/a	n/a
16	SIN3AK20	chr12:50221145-50223047	MCF-7	breast:	n/a	n/a
17	SIN3A	chr12:50220930-50223093	H1-hESC	embryonic stem cell:	n/a	chr12:50222570-50222583 chr12:50221025-50221039
18	POLR2A	chr12:50221988-50223095	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr12:50221880-50223024	HCT-116	colon:	n/a	n/a
20	MAX	chr12:50221201-50223144	A549	lung:	n/a	n/a
21	POLR2A	chr12:50220824-50223264	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50220424..50223939-chr12:50233012..50238065,9	K562	blood:
2	chr12:50216965..50224421-chr12:50234869..50238255,17	MCF-7	breast:
3	chr12:50135126..50137346-chr12:50220595..50223350,3	MCF-7	breast:
4	chr12:50134058..50135690-chr12:50222133..50224042,2	MCF-7	breast:
5	chr12:50222611..50223363-chr16:75681537..75682185,2	NB4	blood:
6	chr12:50134227..50139526-chr12:50218668..50224471,9	K562	blood:
7	chr12:50183912..50186626-chr12:50222654..50225172,2	K562	blood:
8	chr12:50221331..50224259-chr12:50293444..50296232,2	K562	blood:
9	chr12:50133925..50140140-chr12:50217980..50223924,8	K562	blood:
10	chr12:50217971..50224800-chr12:50231213..50239207,27	MCF-7	breast:
11	chr12:50016251..50018773-chr12:50221048..50223022,2	MCF-7	breast:

No data

Variant related genes	Relation type
NCKAP5L	TF binding region
ENSG00000110844	Chromatin interaction
ENSG00000135472	Chromatin interaction
ENSG00000065427	Chromatin interaction
ENSG00000166848	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1031477	0.89[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs10875976	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169166	0.92[ASN][1000 genomes]
rs4898534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4898535	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55677077	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66908137	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7953539	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973894	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11169170	LALBA	cis	cerebellum	SCAN
rs11169170	RPAP3	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50220800-50223200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:50221000-50223200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:50221000-50223400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:50222400-50223200	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr12:50222400-50223200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr12:50222400-50223200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:50222400-50223200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr12:50222400-50223200	Flanking Active TSS	HMEC	breast
9	chr12:50222400-50223400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:50222400-50223400	Flanking Active TSS	Dnd41	blood
11	chr12:50222600-50223200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:50222600-50223200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:50222600-50223200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:50222600-50223200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:50222600-50223200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr12:50222600-50223200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr12:50222600-50223200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:50222600-50223200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr12:50222600-50223200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:50222600-50223200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr12:50222600-50223200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:50222600-50223200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:50222600-50223200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr12:50222600-50223200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:50222600-50223200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:50222600-50223200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:50222600-50223200	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr12:50222600-50223200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:50222600-50223200	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr12:50222600-50223200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr12:50222600-50223200	Flanking Active TSS	Fetal Brain Female	brain
32	chr12:50222600-50223200	Flanking Active TSS	Fetal Heart	heart
33	chr12:50222600-50223200	Flanking Active TSS	Fetal Kidney	kidney
34	chr12:50222600-50223200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr12:50222600-50223200	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr12:50222600-50223200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr12:50222600-50223200	Enhancers	Small Intestine	intestine
38	chr12:50222600-50223200	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr12:50222600-50223200	Flanking Active TSS	A549	lung
40	chr12:50222600-50223200	Flanking Active TSS	Hela-S3	cervix
41	chr12:50222600-50223200	Flanking Active TSS	HepG2	liver
42	chr12:50222600-50223200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr12:50222600-50223200	Flanking Active TSS	NH-A	brain
44	chr12:50222600-50223400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
45	chr12:50222600-50223400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr12:50222600-50223400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr12:50222600-50223400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr12:50222600-50223400	Flanking Active TSS	K562	blood
49	chr12:50222600-50223400	Flanking Active TSS	NHEK	skin
50	chr12:50222800-50223200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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