Variant report

Variant	rs2569754
Chromosome Location	chr19:41936734-41936735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41936590-41937028	U87	brain:	n/a	n/a
2	POLR2A	chr19:41936242-41939720	GM12878	blood:	n/a	n/a
3	CTCF	chr19:41936665-41938558	A549	lung:	n/a	n/a
4	POLR2A	chr19:41936733-41937183	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:41936706-41936771	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:41936609-41937211	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:41936589-41937558	K562	blood:	n/a	n/a
8	POLR2A	chr19:41936609-41939024	K562	blood:	n/a	n/a
9	POLR2A	chr19:41936674-41937048	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:41936662-41937156	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:41936409-41936885	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41936622..41939586-chr19:41947612..41949294,2	K562	blood:
2	chr19:41903978..41906376-chr19:41936347..41938650,2	K562	blood:
3	chr19:41936691..41939385-chr19:41940971..41942681,2	K562	blood:
4	chr19:41858044..41860036-chr19:41936343..41938976,2	MCF-7	breast:
5	chr19:41932975..41939032-chr19:41942824..41947362,11	K562	blood:
6	chr19:41869689..41871301-chr19:41934522..41938582,3	MCF-7	breast:
7	chr19:41854997..41857882-chr19:41936473..41939434,2	K562	blood:
8	chr19:41928996..41931842-chr19:41934329..41936851,2	MCF-7	breast:
9	chr19:41935462..41938566-chr19:41944097..41946991,4	MCF-7	breast:
10	chr19:41927679..41929725-chr19:41935505..41937205,2	MCF-7	breast:

No data

Variant related genes	Relation type
B3GNT8	TF binding region
ENSG00000204978	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000268475	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000123810	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000105329	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10409485	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10413735	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10416743	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10417311	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10417997	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10420556	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10422783	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10422956	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10432268	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1043413	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1077856	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10853751	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11083618	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11083619	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11667848	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11667908	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11668924	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11670583	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11670668	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11670725	0.85[EUR][1000 genomes]
rs11670757	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11880539	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11883104	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12602	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12709849	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12980966	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13344547	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13344563	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13345590	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13346603	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1473248	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs166925	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16975238	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17318596	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17318666	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1967333	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1967334	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2231935	0.83[AMR][1000 genomes]
rs2231940	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241706	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241707	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241708	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241709	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241710	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241711	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2288871	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304242	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2317131	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2569400	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs284648	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs284649	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs284650	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs284651	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284652	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284654	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284655	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284656	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284657	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284658	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284660	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284661	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284662	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284663	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3213860	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3213861	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3745290	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3745292	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3786553	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3810174	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3810175	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816037	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3826713	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4605279	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4674	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802116	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802117	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802118	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803461	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803462	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803463	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803465	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803467	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803468	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803469	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55986560	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58961854	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62117461	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62117462	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508977	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7247332	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7255918	0.84[ASN][1000 genomes]
rs7258973	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8103531	0.85[EUR][1000 genomes]
rs8105833	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs878082	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs878083	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs892044	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9304593	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2569754	B3GNT8	cis	Thyroid	GTEx
rs2569754	B3GNT8	cis	Nerve Tibial	GTEx
rs2569754	CTC-435M10.6	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41932600-41936800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr19:41933200-41938200	Weak transcription	Fetal Kidney	kidney
3	chr19:41933800-41938000	Weak transcription	Psoas Muscle	Psoas
4	chr19:41934000-41936800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:41934000-41944800	Weak transcription	Hela-S3	cervix
6	chr19:41934200-41936800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr19:41934200-41937200	Weak transcription	HepG2	liver
8	chr19:41934200-41937400	Weak transcription	Ovary	ovary
9	chr19:41934200-41937600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:41934200-41938000	Weak transcription	Osteobl	bone
11	chr19:41934200-41938200	Weak transcription	Brain Angular Gyrus	brain
12	chr19:41934400-41936800	Weak transcription	Pancreas	Pancrea
13	chr19:41934400-41939600	Strong transcription	Brain Germinal Matrix	brain
14	chr19:41934400-41945000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr19:41934600-41936800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:41934600-41936800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:41934600-41936800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:41934600-41936800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:41934600-41936800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr19:41934600-41936800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:41934600-41936800	Weak transcription	Gastric	stomach
22	chr19:41934600-41936800	Weak transcription	Right Atrium	heart
23	chr19:41934600-41937000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:41934600-41937000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr19:41934600-41937000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:41934600-41937400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr19:41934600-41937400	Weak transcription	NHLF	lung
28	chr19:41934600-41937600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr19:41934600-41937600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:41934600-41938000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr19:41934600-41938200	Weak transcription	NH-A	brain
32	chr19:41934600-41938200	Weak transcription	NHDF-Ad	bronchial
33	chr19:41934600-41944200	Weak transcription	Fetal Brain Male	brain
34	chr19:41934800-41936800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr19:41934800-41936800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:41934800-41936800	Weak transcription	Adipose Nuclei	Adipose
37	chr19:41934800-41936800	Weak transcription	Placenta	Placenta
38	chr19:41934800-41936800	Weak transcription	HSMMtube	muscle
39	chr19:41934800-41937000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:41934800-41937000	Weak transcription	Esophagus	oesophagus
41	chr19:41934800-41937200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:41934800-41937200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:41934800-41937600	Weak transcription	Fetal Lung	lung
44	chr19:41934800-41937600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr19:41934800-41938200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:41934800-41939600	Strong transcription	Fetal Brain Female	brain
47	chr19:41934800-41945400	Weak transcription	Small Intestine	intestine
48	chr19:41935000-41936800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:41935000-41936800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:41935000-41936800	Weak transcription	Colon Smooth Muscle	Colon

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