Variant report

Variant	rs11168250
Chromosome Location	chr12:48209165-48209166
allele	G/T
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	NFYA	chr12:48209024-48209195	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48208028..48210618-chr17:57914996..57917527,2	MCF-7	breast:
2	chr12:48180173..48182557-chr12:48208551..48210308,2	MCF-7	breast:
3	chr12:48200947..48203542-chr12:48208832..48210426,2	K562	blood:

Variant related genes	Relation type
HDAC7	TF binding region
ENSG00000061273	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11168244	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11168245	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11168251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11168252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55726902	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56389811	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73107980	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73107993	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs875023	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
2	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
3	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	esv3693398	chr12:48186738-48215749	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48203800-48209200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:48204000-48209400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
3	chr12:48204200-48209600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:48205400-48211800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:48206400-48209200	Enhancers	Liver	Liver
6	chr12:48206800-48209400	Enhancers	Small Intestine	intestine
7	chr12:48206800-48209400	Transcr. at gene 5' and 3'	Thymus	Thymus
8	chr12:48207000-48209200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:48207000-48209600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:48207200-48209200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:48207200-48209200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr12:48207200-48209200	Enhancers	Brain Cingulate Gyrus	brain
13	chr12:48207400-48209200	Enhancers	Psoas Muscle	Psoas
14	chr12:48207400-48210200	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr12:48207400-48211400	Weak transcription	Fetal Brain Male	brain
16	chr12:48207600-48209200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:48207600-48209200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:48207600-48209200	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr12:48207600-48209200	Enhancers	Brain Substantia Nigra	brain
20	chr12:48207600-48209200	Genic enhancers	Fetal Stomach	stomach
21	chr12:48207600-48209400	Genic enhancers	Osteobl	bone
22	chr12:48207600-48209600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:48207600-48210600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr12:48207600-48210800	Weak transcription	HepG2	liver
25	chr12:48207600-48211800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr12:48207800-48209200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:48207800-48209200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:48207800-48209200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:48207800-48209200	Genic enhancers	Fetal Muscle Leg	muscle
30	chr12:48207800-48209200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr12:48207800-48209200	Enhancers	Right Atrium	heart
32	chr12:48207800-48209200	Genic enhancers	NHEK	skin
33	chr12:48207800-48209400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr12:48207800-48209600	Enhancers	Brain Hippocampus Middle	brain
35	chr12:48207800-48210000	Enhancers	Colon Smooth Muscle	Colon
36	chr12:48207800-48210200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:48207800-48210600	Enhancers	Left Ventricle	heart
38	chr12:48208000-48209200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:48208000-48209600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:48208000-48209800	Genic enhancers	HUVEC	blood vessel
41	chr12:48208000-48210000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:48208000-48210000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:48208000-48210000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:48208000-48210400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:48208000-48211000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr12:48208000-48211200	Enhancers	Primary B cells from peripheral blood	blood
47	chr12:48208200-48209400	Genic enhancers	K562	blood
48	chr12:48208200-48209400	Genic enhancers	NHLF	lung
49	chr12:48208200-48210200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr12:48208200-48210200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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