Variant report

Variant	rs17019726
Chromosome Location	chr1:212969128-212969129
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	CEBPB	chr1:212969042-212969233	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212963881..212969695-chr1:212970420..212976060,10	K562	blood:
2	chr1:212873187..212876182-chr1:212968130..212971085,2	K562	blood:

Variant related genes	Relation type
NSL1	TF binding region
TATDN3	TF binding region
ENSG00000123685	Chromatin interaction
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10127512	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127703	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127756	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1046083	0.97[EUR][1000 genomes]
rs10863989	0.94[EUR][1000 genomes]
rs10863997	0.89[CEU][hapmap];0.96[GIH][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11120001	0.88[EUR][1000 genomes]
rs11120007	0.97[EUR][1000 genomes]
rs11120014	0.90[GIH][hapmap];0.87[TSI][hapmap]
rs11120017	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11120029	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120030	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120035	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120036	0.91[ASN][1000 genomes]
rs11120042	0.86[YRI][hapmap]
rs11556187	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11800642	0.97[EUR][1000 genomes]
rs11805669	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11806535	0.97[EUR][1000 genomes]
rs11808846	0.90[GIH][hapmap];0.87[TSI][hapmap]
rs11809232	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11809382	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11810895	0.94[EUR][1000 genomes]
rs11811017	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12036054	0.91[ASN][1000 genomes]
rs12128410	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128903	0.95[EUR][1000 genomes]
rs12129933	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12130072	0.94[ASN][1000 genomes]
rs12133124	0.91[ASN][1000 genomes]
rs12136656	0.91[ASN][1000 genomes]
rs12137768	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12140831	0.85[YRI][hapmap]
rs12409787	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12729663	0.94[EUR][1000 genomes]
rs13376317	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13376383	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13376390	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1507357	0.89[CEU][hapmap];0.96[GIH][hapmap];0.89[TSI][hapmap];0.97[EUR][1000 genomes]
rs1507358	0.90[GIH][hapmap];0.87[TSI][hapmap]
rs1532951	0.93[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271148	0.93[GIH][hapmap]
rs2358899	0.97[EUR][1000 genomes]
rs34110137	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35213366	0.90[EUR][1000 genomes]
rs3738798	0.90[GIH][hapmap];0.87[TSI][hapmap]
rs3738803	0.89[CEU][hapmap];0.96[GIH][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55840547	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56088044	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56243109	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59231663	0.95[EUR][1000 genomes]
rs60308869	0.97[EUR][1000 genomes]
rs6540760	0.97[EUR][1000 genomes]
rs6540762	0.90[GIH][hapmap];0.87[TSI][hapmap]
rs6662981	0.94[EUR][1000 genomes]
rs6670648	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6671866	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6681171	0.84[CEU][hapmap];0.94[EUR][1000 genomes]
rs6687672	0.89[CEU][hapmap];0.96[GIH][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6688238	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6694190	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[ASN][1000 genomes]
rs6694448	0.97[EUR][1000 genomes]
rs6700204	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6702101	0.90[GIH][hapmap];0.84[TSI][hapmap]
rs73081853	0.97[EUR][1000 genomes]
rs73081902	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73083707	0.96[EUR][1000 genomes]
rs73083727	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73083731	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73083749	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73083756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083765	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083778	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515115	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516312	0.89[CEU][hapmap];0.96[GIH][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7519582	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524203	0.86[YRI][hapmap]
rs7525518	0.94[EUR][1000 genomes]
rs7527216	0.95[EUR][1000 genomes]
rs7536629	0.94[EUR][1000 genomes]
rs7538755	0.97[EUR][1000 genomes]
rs7544645	0.81[YRI][hapmap]
rs7546462	0.94[EUR][1000 genomes]
rs7546564	0.94[EUR][1000 genomes]
rs7546754	0.96[EUR][1000 genomes]
rs7548861	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552880	0.99[EUR][1000 genomes]
rs7552899	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17019726	TATDN3	cis	multi-tissue	Pritchard
rs17019726	SNFT	cis	multi-tissue	Pritchard
rs17019726	LOC642946	cis	multi-tissue	Pritchard
rs17019726	TATDN3	cis	Artery Tibial	GTEx
rs17019726	FLVCR1	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212971000	Weak transcription	Small Intestine	intestine
2	chr1:212965800-212972000	Weak transcription	Gastric	stomach
3	chr1:212965800-212992600	Weak transcription	Lung	lung
4	chr1:212966000-212970200	Weak transcription	Pancreas	Pancrea
5	chr1:212966000-212972000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:212966000-212974800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:212966000-212981200	Weak transcription	Esophagus	oesophagus
8	chr1:212966000-212983000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
10	chr1:212966200-212970000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:212966200-212971000	Weak transcription	HSMMtube	muscle
12	chr1:212966200-212971800	Weak transcription	Fetal Kidney	kidney
13	chr1:212966200-212972000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:212966200-212973800	Weak transcription	Colonic Mucosa	Colon
15	chr1:212966200-212975600	Weak transcription	HMEC	breast
16	chr1:212966200-212979800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:212966400-212969600	Enhancers	HepG2	liver
18	chr1:212966400-212970000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:212966400-212970000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:212966400-212970000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:212966400-212970000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:212966400-212970000	Weak transcription	Ovary	ovary
23	chr1:212966400-212970200	Weak transcription	Left Ventricle	heart
24	chr1:212966400-212970200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:212966400-212970400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:212966400-212970400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:212966400-212970400	Weak transcription	NH-A	brain
28	chr1:212966400-212972000	Weak transcription	Fetal Brain Female	brain
29	chr1:212966400-212972000	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:212966400-212972000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:212966400-212972000	Weak transcription	Thymus	Thymus
32	chr1:212966400-212977400	Weak transcription	Hela-S3	cervix
33	chr1:212966400-212984000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:212966400-212985600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:212966400-212988200	Weak transcription	Fetal Heart	heart
36	chr1:212966400-212989600	Weak transcription	Fetal Brain Male	brain
37	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
38	chr1:212966600-212969200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:212966600-212969800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:212966600-212970200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:212966600-212970400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:212966600-212970600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:212966800-212969200	Weak transcription	Placenta	Placenta
44	chr1:212966800-212977600	Weak transcription	Brain Germinal Matrix	brain
45	chr1:212966800-212989600	Weak transcription	Psoas Muscle	Psoas
46	chr1:212967000-212969200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:212967000-212969400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:212967000-212969800	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:212967000-212970000	Weak transcription	Adipose Nuclei	Adipose
50	chr1:212967000-212970400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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