Variant report

Variant	rs12178430
Chromosome Location	chr6:27868945-27868946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27856821-27873085	K562	blood:	n/a	n/a
2	POLR2A	chr6:27868917-27870994	K562	blood:	n/a	n/a
3	BCLAF1	chr6:27868004-27869007	K562	blood:	n/a	chr6:27868560-27868569
4	POLR2A	chr6:27856294-27871164	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27868110..27870344-chr6:27873594..27875539,2	MCF-7	breast:
2	chr6:27868875..27870794-chr6:28109566..28111188,2	K562	blood:
3	chr6:27868676..27871582-chr6:27889227..27891930,6	K562	blood:
4	chr6:27867318..27870261-chr6:28091459..28092986,2	MCF-7	breast:
5	chr6:27868230..27870687-chr6:28094988..28097736,2	K562	blood:
6	chr6:26197718..26199629-chr6:27867350..27870167,2	K562	blood:

No data

Variant related genes	Relation type
RNU7-26P	TF binding region
ENSG00000197409	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000196812	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10046419	0.83[ASN][1000 genomes]
rs10046424	0.83[ASN][1000 genomes]
rs12332927	0.81[AFR][1000 genomes]
rs1497525	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1497526	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs16893533	0.83[ASN][1000 genomes]
rs1873212	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1873213	0.93[ASN][1000 genomes]
rs6456803	0.83[EUR][1000 genomes]
rs6900413	0.90[EUR][1000 genomes]
rs73386659	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392694	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73394715	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73394718	0.81[ASN][1000 genomes]
rs7760871	0.83[ASN][1000 genomes]
rs9461420	0.87[ASN][1000 genomes]
rs9461424	0.82[AFR][1000 genomes]
rs9468249	0.83[EUR][1000 genomes]
rs9468250	0.83[EUR][1000 genomes]
rs9468252	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468254	0.87[ASN][1000 genomes]
rs9468255	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9885649	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
3	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
4	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases
5	nsv601209	chr6:27849676-27869321	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	194 gene(s)	inside rSNPs	diseases
6	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12178430	AL022393.7	cis	Artery Tibial	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27863800-27870000	Weak transcription	Primary T cells from cord blood	blood
2	chr6:27863800-27870000	Weak transcription	Adipose Nuclei	Adipose
3	chr6:27863800-27870400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:27864000-27869400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:27864000-27869400	Weak transcription	HMEC	breast
6	chr6:27864000-27869600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:27864000-27870000	Weak transcription	NHEK	skin
8	chr6:27864000-27870200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:27864200-27870000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:27864200-27870400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:27864400-27869600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:27864400-27870000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:27864400-27870000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr6:27864400-27870000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:27864400-27870000	Weak transcription	Fetal Intestine Small	intestine
16	chr6:27864600-27869400	Weak transcription	A549	lung
17	chr6:27864600-27870000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:27864600-27870000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:27864600-27870000	Weak transcription	Fetal Kidney	kidney
20	chr6:27864600-27870000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr6:27864800-27869600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:27865200-27869200	Weak transcription	Dnd41	blood
23	chr6:27865800-27869400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:27865800-27870000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:27866000-27870000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:27866200-27869600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:27866400-27870000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:27867000-27870400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:27867000-27870400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:27867200-27870200	Weak transcription	Placenta	Placenta
31	chr6:27867400-27869200	Weak transcription	Hela-S3	cervix
32	chr6:27867400-27870000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:27867600-27870000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:27867800-27869200	Enhancers	HepG2	liver
35	chr6:27868200-27869000	Flanking Active TSS	GM12878-XiMat	blood
36	chr6:27868200-27869400	Transcr. at gene 5' and 3'	K562	blood
37	chr6:27868600-27870000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:27868600-27870000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:27868600-27870000	Weak transcription	NH-A	brain
40	chr6:27868600-27870000	Weak transcription	Osteobl	bone
41	chr6:27868800-27869600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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