Variant report

Variant	rs9789596
Chromosome Location	chr2:172345282-172345283
allele	C/T
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	chr2:172345219-172345334	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172344598..172348821-chr2:172376554..172380965,4	K562	blood:
2	chr2:172048062..172050725-chr2:172343966..172345491,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DCAF17-1	chr2:172345084-172345288	XLOC_001752

Variant related genes	Relation type
ENSG00000234061	TF binding region
DAP3P2	TF binding region
ENSG00000071967	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10445722	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10515933	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12151641	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1558936	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17220419	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17220440	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17220608	0.94[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17220657	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17220699	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17220734	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17221367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17221402	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17221619	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17286415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17286660	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1861899	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1981788	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2356781	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36112363	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3731981	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3731982	0.93[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3731983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731985	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3795998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4417688	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4458186	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4496302	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4522571	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4668385	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4668386	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4668387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56410960	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57099324	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58536060	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59960186	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60439518	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62181352	0.87[AFR][1000 genomes]
rs62183467	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183468	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62183470	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62183471	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62183472	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183492	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62183493	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183494	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183495	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183497	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183498	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183499	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183502	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183503	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183506	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183507	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433290	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433292	0.93[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6713612	0.94[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6720250	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6740733	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6741806	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6743290	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7562674	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs7568037	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7572334	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7576894	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7598137	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7606658	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9678149	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9678164	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9679537	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9789572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9789596	METTL8	cis	Esophagus Muscularis	GTEx
rs9789596	CYBRD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172306000-172348000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:172309600-172348400	Weak transcription	Fetal Heart	heart
3	chr2:172327000-172346800	Weak transcription	Colonic Mucosa	Colon
4	chr2:172327200-172346600	Weak transcription	Thymus	Thymus
5	chr2:172327200-172348800	Weak transcription	Spleen	Spleen
6	chr2:172327400-172346800	Weak transcription	Hela-S3	cervix
7	chr2:172327400-172347600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:172327800-172346000	Weak transcription	Fetal Brain Male	brain
9	chr2:172330400-172346200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:172331400-172345800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:172333400-172345400	Weak transcription	NHDF-Ad	bronchial
12	chr2:172333400-172347800	Weak transcription	Brain Angular Gyrus	brain
13	chr2:172334600-172349200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:172334800-172346200	Weak transcription	Psoas Muscle	Psoas
15	chr2:172334800-172346800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:172334800-172347200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:172334800-172349200	Weak transcription	Esophagus	oesophagus
18	chr2:172335200-172346400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:172335400-172349000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:172337800-172348000	Weak transcription	Brain Substantia Nigra	brain
21	chr2:172338000-172345600	Weak transcription	Fetal Thymus	thymus
22	chr2:172338000-172349400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:172338200-172347000	Weak transcription	HMEC	breast
24	chr2:172338400-172349800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:172338600-172345400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:172339600-172345400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:172339600-172347800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:172339600-172348000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:172339800-172348000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:172339800-172350600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr2:172339800-172352200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:172340000-172345400	Weak transcription	Fetal Intestine Large	intestine
33	chr2:172340000-172347000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:172340000-172347800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:172340000-172348000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:172340000-172348000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:172340000-172348000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:172340000-172348600	Weak transcription	Ovary	ovary
39	chr2:172340000-172351200	Weak transcription	Aorta	Aorta
40	chr2:172340000-172368400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:172340400-172348000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:172341000-172348000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:172342200-172347000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:172342200-172348200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:172342200-172348600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:172344400-172345400	Enhancers	NHEK	skin
47	chr2:172344600-172346000	ZNF genes & repeats	Primary T cells from cord blood	blood
48	chr2:172344600-172346000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:172344800-172345400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
50	chr2:172344800-172345600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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