Variant report

Variant	rs13231375
Chromosome Location	chr7:138143811-138143812
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:138143578-138144133	HepG2	liver:	n/a	n/a
2	NANOG	chr7:138143383-138143875	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:138143131-138146474	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr7:138143701-138143932	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr7:138143390-138144021	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr7:138143598-138143932	HepG2	liver:	n/a	n/a
7	SIN3A	chr7:138143356-138143996	H1-hESC	embryonic stem cell:	n/a	n/a
8	TAF1	chr7:138143356-138144005	H1-hESC	embryonic stem cell:	n/a	n/a
9	POU5F1	chr7:138143366-138143832	H1-hESC	embryonic stem cell:	n/a	n/a
10	TBP	chr7:138143356-138146080	H1-hESC	embryonic stem cell:	n/a	n/a
11	RFX5	chr7:138143135-138147159	SK-N-SH	brain:	n/a	chr7:138144908-138144923
12	EP300	chr7:138143351-138143930	H1-hESC	embryonic stem cell:	n/a	n/a
13	RAD21	chr7:138143453-138144037	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr7:138143320-138144010	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr7:138143236-138144106	H1-hESC	embryonic stem cell:	n/a	chr7:138143743-138143755
16	HDAC2	chr7:138143314-138143882	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr7:138143486-138144177	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr7:138143331-138144099	H1-hESC	embryonic stem cell:	n/a	n/a
19	ATF2	chr7:138143320-138144019	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr7:138143301-138143973	H1-hESC	embryonic stem cell:	n/a	n/a
21	CHD2	chr7:138143362-138144082	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr7:138143465-138143919	H1-hESC	embryonic stem cell:	n/a	n/a
23	JUND	chr7:138143522-138144130	H1-hESC	embryonic stem cell:	n/a	chr7:138143917-138143928 chr7:138143742-138143751
24	TAF1	chr7:138143279-138143965	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr7:138143339-138144047	H1-hESC	embryonic stem cell:	n/a	n/a
26	CHD1	chr7:138143330-138144695	H1-hESC	embryonic stem cell:	n/a	n/a
27	SP1	chr7:138143352-138144015	H1-hESC	embryonic stem cell:	n/a	n/a
28	GTF2F1	chr7:138143448-138143988	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr7:138143324-138143951	H1-hESC	embryonic stem cell:	n/a	n/a
30	E2F6	chr7:138143527-138143969	H1-hESC	embryonic stem cell:	n/a	chr7:138143743-138143755
31	ATF2	chr7:138143261-138144814	H1-hESC	embryonic stem cell:	n/a	n/a
32	YY1	chr7:138143363-138143962	H1-hESC	embryonic stem cell:	n/a	n/a
33	TAF7	chr7:138143332-138146199	H1-hESC	embryonic stem cell:	n/a	n/a
34	SP4	chr7:138143350-138144075	H1-hESC	embryonic stem cell:	n/a	n/a
35	TCF12	chr7:138143402-138143860	H1-hESC	embryonic stem cell:	n/a	n/a
36	SP1	chr7:138143388-138144071	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr7:138143331-138143971	H1-hESC	embryonic stem cell:	n/a	n/a
38	EP300	chr7:138143525-138143900	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:138142373..138144059-chr7:138148709..138151590,2	MCF-7	breast:
2	chr7:138123228..138126392-chr7:138142592..138145835,3	K562	blood:
3	chr7:138143601..138146619-chr7:138166848..138169714,4	K562	blood:
4	chr7:138129342..138131930-chr7:138142283..138144640,2	K562	blood:

No data

Variant related genes	Relation type
TRIM24	TF binding region
ENSG00000239123	Chromatin interaction
ENSG00000214815	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10279876	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763093	1.00[ASN][1000 genomes]
rs11773577	1.00[ASN][1000 genomes]
rs12707387	1.00[ASN][1000 genomes]
rs12707388	1.00[ASN][1000 genomes]
rs13230953	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236259	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13242427	1.00[ASN][1000 genomes]
rs34718165	1.00[ASN][1000 genomes]
rs35558871	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35674497	1.00[ASN][1000 genomes]
rs55918517	1.00[ASN][1000 genomes]
rs6467777	1.00[ASN][1000 genomes]
rs6467781	1.00[ASN][1000 genomes]
rs67586210	1.00[ASN][1000 genomes]
rs6970145	1.00[ASN][1000 genomes]
rs7782453	1.00[ASN][1000 genomes]
rs7799818	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7803989	1.00[ASN][1000 genomes]
rs7811152	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831153	chr7:138078179-138265648	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13231375	ADCK2	cis	parietal	SCAN
rs13231375	ADCK2	cis	cerebellum	SCAN
rs13231375	TAS2R4	cis	parietal	SCAN
rs13231375	KLRG2	cis	parietal	SCAN
rs13231375	TPST1	trans	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138140600-138144200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:138140600-138144200	Weak transcription	Fetal Intestine Large	intestine
3	chr7:138141200-138144200	Weak transcription	Liver	Liver
4	chr7:138141200-138144400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:138141200-138144400	Weak transcription	Right Atrium	heart
6	chr7:138141400-138145000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:138142600-138144200	Enhancers	HepG2	liver
8	chr7:138142800-138144400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:138143200-138144200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:138143200-138144200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:138143400-138144000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:138143400-138144200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:138143400-138144600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr7:138143400-138148400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:138143600-138144000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr7:138143600-138144200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:138143600-138144200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr7:138143600-138146000	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr7:138143600-138146600	Active TSS	H1 Cell Line	embryonic stem cell
20	chr7:138143600-138148000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr7:138143600-138148000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr7:138143600-138148000	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr7:138143600-138149000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr7:138143600-138150200	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr7:138143800-138144000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr7:138143800-138144000	ZNF genes & repeats	K562	blood
27	chr7:138143800-138144200	Enhancers	Primary T cells from cord blood	blood
28	chr7:138143800-138144200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr7:138143800-138144200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:138143800-138144200	Enhancers	Dnd41	blood
31	chr7:138143800-138144600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr7:138143800-138146400	Active TSS	NH-A	brain
33	chr7:138143800-138147000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:138143800-138147400	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr7:138143800-138148000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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