Variant report

Variant	rs10875996
Chromosome Location	chr12:50478352-50478353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:50478292-50479283	SK-N-SH	brain:	n/a	chr12:50478890-50478903
2	POLR2A	chr12:50477999-50480078	HepG2	liver:	n/a	n/a
3	CHD1	chr12:50478135-50479792	IMR90	lung:	n/a	n/a
4	MXI1	chr12:50478105-50480000	SK-N-SH	brain:	n/a	n/a
5	TEAD4	chr12:50478345-50479485	ECC-1	luminal epithelium:	n/a	n/a
6	MAX	chr12:50478351-50479543	MCF-7	breast:	n/a	chr12:50478768-50478777
7	SIX5	chr12:50478263-50479087	A549	lung:	n/a	n/a
8	FOSL2	chr12:50478325-50479066	A549	lung:	n/a	n/a
9	HCFC1	chr12:50478275-50480063	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr12:50478152-50479433	IMR90	lung:	n/a	n/a
11	NFIC	chr12:50478298-50479152	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:50476634..50479276-chr12:50493202..50495258,2	K562	blood:
2	chr12:50477150..50481052-chr12:50559881..50562931,6	MCF-7	breast:
3	chr12:50477499..50479020-chr12:50528748..50530881,2	MCF-7	breast:
4	chr12:50477720..50479464-chr12:50594213..50596665,2	MCF-7	breast:
5	chr12:50466696..50474949-chr12:50474970..50481457,17	MCF-7	breast:
6	chr12:50279366..50281726-chr12:50476723..50478563,2	MCF-7	breast:
7	chr12:50472028..50474859-chr12:50477717..50480636,3	MCF-7	breast:
8	chr12:50477580..50479686-chr17:62501151..62502654,2	MCF-7	breast:
9	chr12:50478149..50480392-chr17:58677532..58679268,2	MCF-7	breast:
10	chr12:50477670..50481382-chr12:50495555..50500836,7	K562	blood:
11	chr12:50475132..50479699-chr12:50479828..50484275,5	K562	blood:
12	chr12:50477885..50480264-chr12:50559751..50562542,2	K562	blood:
13	chr12:50477576..50479559-chr12:50526628..50528314,2	MCF-7	breast:
14	chr12:50475972..50484033-chr12:50500850..50507517,14	K562	blood:
15	chr12:50477100..50479136-chr12:50582674..50585443,2	K562	blood:
16	chr12:50477567..50484756-chr12:50559008..50565131,16	MCF-7	breast:
17	chr12:50475910..50478397-chr12:50494395..50497008,2	K562	blood:
18	chr12:50461826..50464798-chr12:50477927..50479451,2	K562	blood:
19	chr12:50477688..50480373-chr12:50497434..50499573,3	K562	blood:
20	chr12:50477178..50480105-chr12:50648113..50650406,2	K562	blood:
21	chr12:50464456..50466840-chr12:50477683..50480596,2	MCF-7	breast:

No data

Variant related genes	Relation type
SMARCD1	TF binding region
ENSG00000257298	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000167588	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000212496	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000170836	Chromatin interaction
ENSG00000050405	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10875995	0.83[EUR][1000 genomes]
rs11169270	0.88[EUR][1000 genomes]
rs376184	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4898546	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56990521	0.83[EUR][1000 genomes]
rs590460	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs685012	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs706794	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs836175	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs836178	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	esv3437172	chr12:50478110-50480658	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50464800-50478400	Weak transcription	Primary T cells from cord blood	blood
2	chr12:50475200-50478400	Weak transcription	Lung	lung
3	chr12:50477400-50478400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:50477800-50479400	Active TSS	Dnd41	blood
5	chr12:50478000-50478400	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:50478000-50478600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:50478000-50478800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:50478000-50479600	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr12:50478000-50480200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:50478200-50478400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
11	chr12:50478200-50478400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:50478200-50478400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:50478200-50478400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:50478200-50478400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:50478200-50478400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:50478200-50478400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:50478200-50478400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr12:50478200-50478400	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr12:50478200-50478400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:50478200-50478400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:50478200-50478400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:50478200-50478400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr12:50478200-50478400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr12:50478200-50478400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr12:50478200-50478400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr12:50478200-50478400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr12:50478200-50478400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:50478200-50478400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr12:50478200-50478400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:50478200-50478400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:50478200-50478400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:50478200-50478400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:50478200-50478400	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr12:50478200-50478400	Flanking Active TSS	Liver	Liver
35	chr12:50478200-50478400	Enhancers	Brain Angular Gyrus	brain
36	chr12:50478200-50478400	Enhancers	Brain Anterior Caudate	brain
37	chr12:50478200-50478400	Enhancers	Brain Cingulate Gyrus	brain
38	chr12:50478200-50478400	Enhancers	Brain Hippocampus Middle	brain
39	chr12:50478200-50478400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr12:50478200-50478400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:50478200-50478400	Enhancers	Brain Substantia Nigra	brain
42	chr12:50478200-50478400	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr12:50478200-50478400	Enhancers	Fetal Brain Male	brain
44	chr12:50478200-50478400	Enhancers	Fetal Heart	heart
45	chr12:50478200-50478400	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr12:50478200-50478400	Flanking Active TSS	Fetal Muscle Trunk	muscle
47	chr12:50478200-50478400	Flanking Active TSS	Fetal Stomach	stomach
48	chr12:50478200-50478400	Enhancers	Placenta Amnion	Placenta Amnion
49	chr12:50478200-50478400	Flanking Active TSS	Right Ventricle	heart
50	chr12:50478200-50478400	Enhancers	Sigmoid Colon	Sigmoid Colon

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