Variant report

Variant	rs11169172
Chromosome Location	chr12:50232169-50232170
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50217971..50224800-chr12:50231213..50239207,27	MCF-7	breast:
2	chr12:50142342..50144215-chr12:50231423..50233388,2	K562	blood:
3	chr12:50170142..50172988-chr12:50230634..50232481,2	MCF-7	breast:
4	chr12:50019300..50020807-chr12:50231551..50233204,2	K562	blood:
5	chr12:50170407..50172226-chr12:50230381..50232987,2	K562	blood:
6	chr12:50098843..50101538-chr12:50231874..50234864,2	K562	blood:
7	chr12:50222103..50225028-chr12:50228946..50232862,3	MCF-7	breast:
8	chr12:50220758..50227724-chr12:50229554..50234634,11	K562	blood:
9	chr12:50229987..50234599-chr12:50234805..50237897,8	MCF-7	breast:
10	chr12:50029476..50031392-chr12:50231608..50233910,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000186666	Chromatin interaction
ENSG00000167566	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000258057	Chromatin interaction
ENSG00000161791	Chromatin interaction
ENSG00000110844	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11169153	0.82[AMR][1000 genomes]
rs11169154	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs11169160	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes]
rs1470907	0.85[AMR][1000 genomes]
rs3741554	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs3741555	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.87[AMR][1000 genomes]
rs3813526	1.00[CEU][hapmap];0.88[CHD][hapmap];0.87[AMR][1000 genomes]
rs4898531	0.84[AMR][1000 genomes]
rs4898533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4898538	0.86[YRI][hapmap]
rs56690720	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59429669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134749	0.83[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs897059	1.00[CEU][hapmap];0.93[CHD][hapmap];0.80[LWK][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11169172	BCDIN3D,LOC100286844	cis	brain	BrainEAC

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50222800-50235400	Weak transcription	Ovary	ovary
2	chr12:50222800-50236200	Weak transcription	Aorta	Aorta
3	chr12:50223000-50234600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:50223000-50234600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:50223000-50235000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:50223000-50235400	Weak transcription	Brain Anterior Caudate	brain
7	chr12:50223000-50235400	Weak transcription	Left Ventricle	heart
8	chr12:50223000-50235600	Weak transcription	Brain Substantia Nigra	brain
9	chr12:50223000-50236000	Weak transcription	Lung	lung
10	chr12:50223200-50235200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:50223200-50235200	Weak transcription	Liver	Liver
12	chr12:50223200-50235200	Weak transcription	HSMM	muscle
13	chr12:50223200-50235400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:50223200-50235400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:50223200-50235400	Weak transcription	Adipose Nuclei	Adipose
16	chr12:50223200-50235400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:50223200-50235400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:50223200-50235400	Weak transcription	Thymus	Thymus
19	chr12:50223200-50235400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr12:50223200-50235400	Weak transcription	NHDF-Ad	bronchial
21	chr12:50223200-50235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:50223400-50232200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:50223400-50232600	Weak transcription	Fetal Thymus	thymus
24	chr12:50223400-50233200	Weak transcription	A549	lung
25	chr12:50223400-50234600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:50223400-50235000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:50223400-50235000	Weak transcription	Primary T cells from cord blood	blood
28	chr12:50223400-50235000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:50223400-50235000	Weak transcription	Hela-S3	cervix
30	chr12:50223400-50235200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:50223400-50235200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr12:50223400-50235200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:50223400-50235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:50223400-50235200	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:50223400-50235200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:50223400-50235200	Weak transcription	Fetal Intestine Large	intestine
37	chr12:50223400-50235200	Weak transcription	Fetal Intestine Small	intestine
38	chr12:50223400-50235200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr12:50223400-50235400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr12:50223400-50235400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:50223400-50235400	Weak transcription	Fetal Lung	lung
42	chr12:50223400-50235400	Weak transcription	Fetal Stomach	stomach
43	chr12:50223400-50235600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:50223400-50235600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:50223400-50235600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:50223400-50235600	Weak transcription	Gastric	stomach
47	chr12:50223400-50235600	Weak transcription	Right Atrium	heart
48	chr12:50227000-50235000	Weak transcription	HMEC	breast
49	chr12:50227000-50235400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:50227200-50232200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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