Variant report

Variant	rs28735279
Chromosome Location	chr12:49249546-49249547
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	POLR2A	chr12:49248208-49252609	A549	lung:	n/a	n/a
2	POLR2A	chr12:49249387-49249581	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49243837..49250262-chr12:49279824..49286856,16	MCF-7	breast:
2	chr12:49245861..49248641-chr12:49249429..49251166,2	MCF-7	breast:
3	chr12:49203980..49213270-chr12:49239370..49250118,15	MCF-7	breast:

Variant related genes	Relation type
DDX23	TF binding region
ENSG00000199394	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000167535	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11168756	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11168758	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61941109	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv826363	chr12:49177227-49250989	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49246600-49250600	Weak transcription	Lung	lung
2	chr12:49246600-49251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:49246600-49251200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:49246600-49251200	Weak transcription	Gastric	stomach
5	chr12:49246600-49251200	Weak transcription	Spleen	Spleen
6	chr12:49246600-49258600	Weak transcription	Small Intestine	intestine
7	chr12:49246800-49251400	Weak transcription	Pancreas	Pancrea
8	chr12:49246800-49256400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:49247000-49251200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:49247000-49251200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:49247000-49251400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:49247000-49254600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:49247200-49250000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:49247200-49250200	Weak transcription	Brain Germinal Matrix	brain
15	chr12:49247200-49250400	Weak transcription	Fetal Stomach	stomach
16	chr12:49247200-49250600	Weak transcription	Fetal Intestine Small	intestine
17	chr12:49247200-49251200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:49247200-49251200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:49247200-49251200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:49247200-49251200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:49247200-49251200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:49247200-49251200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:49247200-49251200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:49247200-49251200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:49247200-49251200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:49247200-49251200	Weak transcription	Liver	Liver
27	chr12:49247200-49251200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:49247200-49251200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:49247200-49251200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:49247200-49251200	Weak transcription	GM12878-XiMat	blood
31	chr12:49247200-49251400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:49247200-49251400	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:49247200-49251400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:49247200-49253200	Weak transcription	HepG2	liver
35	chr12:49247200-49254200	Weak transcription	Fetal Intestine Large	intestine
36	chr12:49247200-49254600	Weak transcription	Adipose Nuclei	Adipose
37	chr12:49247200-49254600	Weak transcription	Brain Angular Gyrus	brain
38	chr12:49247200-49254600	Weak transcription	Fetal Brain Male	brain
39	chr12:49247200-49254800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:49247200-49254800	Weak transcription	Primary B cells from cord blood	blood
41	chr12:49247200-49255000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:49247200-49255400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:49247200-49255600	Weak transcription	Colonic Mucosa	Colon
44	chr12:49247200-49255800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:49247200-49255800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:49247200-49256000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:49247200-49256600	Weak transcription	Primary T cells from cord blood	blood
48	chr12:49247200-49257000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:49247200-49257800	Weak transcription	Stomach Mucosa	stomach
50	chr12:49247200-49258000	Weak transcription	Brain Substantia Nigra	brain

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