Variant report

Variant	rs11809232
Chromosome Location	chr1:212964427-212964428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:212964280-212964572	K562	blood:	n/a	n/a
2	HCFC1	chr1:212964274-212965855	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:212964316-212965680	K562	blood:	n/a	n/a
4	CBX3	chr1:212964336-212965731	K562	blood:	n/a	n/a
5	REST	chr1:212964363-212966008	H1-neurons	neurons:	n/a	n/a
6	TEAD4	chr1:212964287-212965710	K562	blood:	n/a	n/a
7	MXI1	chr1:212964236-212966381	SK-N-SH	brain:	n/a	n/a
8	TFAP2C	chr1:212964363-212965761	Hela-S3	cervix:	n/a	n/a
9	UBTF	chr1:212964321-212965868	K562	blood:	n/a	n/a
10	TAF1	chr1:212964200-212964485	K562	blood:	n/a	n/a
11	TBP	chr1:212964347-212965722	K562	blood:	n/a	chr1:212965331-212965342
12	YY1	chr1:212964301-212964465	K562	blood:	n/a	n/a
13	UBTF	chr1:212964357-212965733	K562	blood:	n/a	n/a
14	GTF3C2	chr1:212964286-212964887	Hela-S3	cervix:	n/a	n/a
15	TBL1XR1	chr1:212964353-212964538	K562	blood:	n/a	n/a
16	MYC	chr1:212964347-212965710	K562	blood:	n/a	chr1:212965428-212965438
17	MAZ	chr1:212964387-212965774	IMR90	lung:	n/a	chr1:212965428-212965438
18	MYC	chr1:212964354-212965696	K562	blood:	n/a	chr1:212965428-212965438
19	SIX5	chr1:212964379-212965545	A549	lung:	n/a	n/a
20	POLR2A	chr1:212964407-212965759	K562	blood:	n/a	n/a
21	MXI1	chr1:212964277-212965909	IMR90	lung:	n/a	n/a
22	MXI1	chr1:212964388-212964655	Hela-S3	cervix:	n/a	n/a
23	NR2F2	chr1:212964123-212966130	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212963280..212966676-chr1:213030010..213031803,4	K562	blood:
2	chr1:212780353..212782606-chr1:212962286..212965026,4	K562	blood:
3	chr1:212963050..212964812-chr1:213052963..213055078,2	K562	blood:
4	chr1:212963881..212969695-chr1:212970420..212976060,10	K562	blood:
5	chr1:212779632..212786722-chr1:212963640..212968604,10	K562	blood:
6	chr1:212525375..212527593-chr1:212964320..212966298,2	MCF-7	breast:
7	chr1:212962817..212964825-chr1:212966481..212969163,3	K562	blood:
8	chr1:212586665..212588349-chr1:212964322..212966191,2	MCF-7	breast:

No data

Variant related genes	Relation type
TATDN3	TF binding region
ENSG00000201544	Chromatin interaction
ENSG00000198468	Chromatin interaction
ENSG00000162769	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000065600	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10127512	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10127703	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10127756	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1046083	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10863989	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10863997	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120001	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120007	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11120010	0.81[ASN][1000 genomes]
rs11120014	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11120017	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120018	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11120029	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11120030	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11120035	0.82[EUR][1000 genomes]
rs11556187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800642	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11805669	0.82[EUR][1000 genomes]
rs11806535	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11808846	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11809382	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11810895	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11811017	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12119531	0.86[ASN][1000 genomes]
rs12128410	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12128903	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12129465	0.81[ASN][1000 genomes]
rs12129933	0.84[EUR][1000 genomes]
rs12133174	0.81[ASN][1000 genomes]
rs12137768	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12139618	0.86[ASN][1000 genomes]
rs12145131	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12402370	0.97[ASN][1000 genomes]
rs12404618	0.81[ASN][1000 genomes]
rs12404885	0.81[ASN][1000 genomes]
rs12406499	0.86[ASN][1000 genomes]
rs12729663	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13376317	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13376383	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13376390	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1507357	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1507358	0.81[ASN][1000 genomes]
rs1532951	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17019726	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1857971	0.81[ASN][1000 genomes]
rs2174780	0.89[ASN][1000 genomes]
rs2271148	0.89[ASN][1000 genomes]
rs2358899	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34110137	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35213366	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3738798	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3738803	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55840547	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56088044	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56243109	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57449384	0.97[ASN][1000 genomes]
rs58203936	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59231663	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60308869	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61736926	0.88[ASN][1000 genomes]
rs6540760	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6540762	0.81[ASN][1000 genomes]
rs6657089	0.86[ASN][1000 genomes]
rs6662981	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6670648	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671866	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681171	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6687672	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688238	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6694448	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6700204	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081853	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73081902	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73083705	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73083707	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73083727	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73083731	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73083743	1.00[ASN][1000 genomes]
rs73083749	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083756	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73083765	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73083778	0.84[EUR][1000 genomes]
rs7515115	0.84[EUR][1000 genomes]
rs7516312	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7519582	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7525518	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7527216	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7536629	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7538755	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7546462	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7546564	0.94[EUR][1000 genomes]
rs7546754	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7548861	0.96[EUR][1000 genomes]
rs7552880	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1010003	chr1:212944240-212986996	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11809232	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs11809232	TATDN3	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
2	chr1:212895600-212964600	Weak transcription	Gastric	stomach
3	chr1:212960400-212964600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:212962400-212966000	Active TSS	K562	blood
5	chr1:212963200-212966000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:212963200-212966200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:212963200-212966600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:212963400-212966400	Active TSS	Rectal Smooth Muscle	rectum
9	chr1:212963600-212966400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:212963800-212964600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr1:212963800-212964600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr1:212963800-212966000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:212963800-212966000	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr1:212963800-212966000	Active TSS	A549	lung
15	chr1:212963800-212966200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:212963800-212966200	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr1:212963800-212966200	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr1:212963800-212966400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:212963800-212966400	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:212963800-212966600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:212964000-212965200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:212964000-212966000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:212964000-212966000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:212964000-212966000	Active TSS	Hela-S3	cervix
25	chr1:212964000-212966200	Active TSS	Colon Smooth Muscle	Colon
26	chr1:212964000-212966200	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:212964200-212964600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:212964200-212964600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr1:212964200-212964600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr1:212964200-212964600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:212964200-212964600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr1:212964200-212964600	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr1:212964200-212964600	Flanking Active TSS	Fetal Stomach	stomach
34	chr1:212964200-212964600	Flanking Active TSS	Fetal Thymus	thymus
35	chr1:212964200-212964600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr1:212964200-212964600	Weak transcription	Small Intestine	intestine
37	chr1:212964200-212964600	Flanking Active TSS	HUVEC	blood vessel
38	chr1:212964200-212964600	Flanking Active TSS	Osteobl	bone
39	chr1:212964200-212964800	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr1:212964200-212964800	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr1:212964200-212964800	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr1:212964200-212964800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:212964200-212964800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:212964200-212964800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr1:212964200-212964800	Active TSS	Brain Germinal Matrix	brain
46	chr1:212964200-212965000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:212964200-212965000	Active TSS	Right Atrium	heart
48	chr1:212964200-212965800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr1:212964200-212965800	Active TSS	NHDF-Ad	bronchial
50	chr1:212964200-212966000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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