Variant report

Variant	rs62117462
Chromosome Location	chr19:41900813-41900814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU2F2	chr19:41900433-41900851	GM12891	blood:	n/a	n/a
2	PAX5	chr19:41900543-41900903	GM12878	blood:	n/a	n/a
3	RUNX3	chr19:41900303-41901407	GM12878	blood:	n/a	n/a
4	FOXM1	chr19:41900443-41900891	GM12878	blood:	n/a	n/a
5	EP300	chr19:41900610-41900931	GM12878	blood:	n/a	n/a
6	NFIC	chr19:41900341-41900890	GM12878	blood:	n/a	n/a
7	MTA3	chr19:41900279-41900825	GM12878	blood:	n/a	n/a
8	EBF1	chr19:41900365-41900892	GM12878	blood:	n/a	n/a
9	RUNX3	chr19:41900296-41901000	GM12878	blood:	n/a	n/a
10	TCF3	chr19:41900510-41900866	GM12878	blood:	n/a	n/a
11	PAX5	chr19:41900343-41900890	GM12878	blood:	n/a	n/a
12	PAX5	chr19:41900441-41900852	GM12878	blood:	n/a	n/a
13	TCF12	chr19:41900589-41900877	GM12878	blood:	n/a	n/a
14	NFIC	chr19:41900251-41901188	GM12878	blood:	n/a	n/a
15	BCL11A	chr19:41900416-41900922	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:41900422-41900885	GM12878	blood:	n/a	n/a
17	FOXM1	chr19:41900356-41900960	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41899828..41905293-chr19:41906916..41917787,16	MCF-7	breast:
2	chr19:41895688..41899126-chr19:41900060..41902495,3	MCF-7	breast:
3	chr19:41889940..41893825-chr19:41898785..41901316,3	K562	blood:
4	chr19:41893973..41895483-chr19:41898970..41901423,2	K562	blood:
5	chr19:41868160..41871597-chr19:41899998..41904284,10	K562	blood:

No data

Variant related genes	Relation type
BCKDHA	TF binding region
ENSG00000268987	TF binding region
ENSG00000123810	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000142046	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10409485	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10413735	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10416743	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10417311	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10417997	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420556	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10422783	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10422956	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10432268	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1043413	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1077856	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10853751	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11083618	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083619	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11667848	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11667908	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668924	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11670583	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11670668	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11670725	0.88[EUR][1000 genomes]
rs11670757	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11880539	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11883104	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12602	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12709849	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12980966	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12982607	0.85[ASN][1000 genomes]
rs13344547	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13344563	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13345590	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13346603	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1473248	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs166925	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16975238	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17318596	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17318666	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1967333	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1967334	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2231940	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2241706	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241707	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241708	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241709	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241710	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241711	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288871	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304242	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2317131	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2569400	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2569754	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs284648	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284649	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284650	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284651	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284652	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284654	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284655	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284656	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284657	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284658	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284660	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284661	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284662	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs284663	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3213860	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3213861	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3745290	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3745292	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3786553	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3810174	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3810175	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816037	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3826713	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4605279	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4674	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802116	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802117	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802118	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803461	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803462	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803463	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803465	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803467	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803468	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803469	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55986560	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58961854	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62117461	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6508977	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247332	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7255918	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7258973	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8103531	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8105450	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8105833	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs878082	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs878083	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs892044	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9304593	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62117462	B3GNT8	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41883000-41902800	Weak transcription	Stomach Mucosa	stomach
2	chr19:41883200-41901400	Weak transcription	Fetal Brain Male	brain
3	chr19:41883200-41902600	Weak transcription	Right Atrium	heart
4	chr19:41883200-41902800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:41883200-41902800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:41884600-41902400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:41886400-41902800	Weak transcription	NHDF-Ad	bronchial
8	chr19:41887600-41901600	Strong transcription	Fetal Intestine Small	intestine
9	chr19:41887800-41901400	Strong transcription	Fetal Stomach	stomach
10	chr19:41888000-41901200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr19:41893200-41901400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:41896600-41902600	Weak transcription	Small Intestine	intestine
13	chr19:41896800-41902400	Weak transcription	HUVEC	blood vessel
14	chr19:41897000-41901200	Weak transcription	Hela-S3	cervix
15	chr19:41897400-41902400	Weak transcription	Fetal Lung	lung
16	chr19:41897600-41902400	Weak transcription	Psoas Muscle	Psoas
17	chr19:41897600-41902600	Weak transcription	HSMMtube	muscle
18	chr19:41897800-41901000	Weak transcription	K562	blood
19	chr19:41897800-41901800	Weak transcription	NH-A	brain
20	chr19:41897800-41902200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:41897800-41902400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:41897800-41902400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr19:41897800-41902400	Weak transcription	Fetal Kidney	kidney
24	chr19:41897800-41902800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:41898000-41901400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:41898000-41901400	Weak transcription	Brain Angular Gyrus	brain
27	chr19:41898000-41901400	Weak transcription	Pancreas	Pancrea
28	chr19:41898000-41901600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:41898000-41901600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr19:41898000-41901800	Weak transcription	Brain Hippocampus Middle	brain
31	chr19:41898000-41902000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:41898000-41902200	Weak transcription	HSMM	muscle
33	chr19:41898000-41902400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:41898000-41902400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr19:41898000-41902400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr19:41898000-41902400	Weak transcription	HMEC	breast
37	chr19:41898000-41902800	Weak transcription	Colon Smooth Muscle	Colon
38	chr19:41898000-41902800	Weak transcription	NHLF	lung
39	chr19:41898200-41901000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr19:41898200-41901200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:41898200-41901200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:41898200-41901200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:41898200-41901200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:41898200-41901200	Weak transcription	Fetal Thymus	thymus
45	chr19:41898200-41901200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:41898200-41901400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:41898200-41901400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr19:41898200-41901400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:41898200-41901400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr19:41898200-41901400	Weak transcription	Duodenum Mucosa	Duodenum

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