Variant report

Variant	rs10417311
Chromosome Location	chr19:41902038-41902039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41901158-41902059	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:41901903-41902112	K562	blood:	n/a	n/a
3	POLR2A	chr19:41901105-41902335	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:41899828..41905293-chr19:41906916..41917787,16	MCF-7	breast:
2	chr19:41815990..41817853-chr19:41901729..41903326,2	K562	blood:
3	chr19:41861983..41864638-chr19:41901106..41902845,2	K562	blood:
4	chr19:41856329..41860180-chr19:41901826..41904297,4	K562	blood:
5	chr19:41895688..41899126-chr19:41900060..41902495,3	MCF-7	breast:
6	chr19:41855447..41861218-chr19:41901143..41905435,7	MCF-7	breast:
7	chr19:41868160..41871597-chr19:41899998..41904284,10	K562	blood:
8	chr19:41901938..41905441-chr19:41944047..41947443,5	K562	blood:
9	chr19:41901991..41905119-chr19:41933008..41936084,3	MCF-7	breast:
10	chr19:41855237..41861298-chr19:41901562..41905286,5	K562	blood:

No data

Variant related genes	Relation type
BCKDHA	TF binding region
ENSG00000268987	TF binding region
ENSG00000255730	Chromatin interaction
ENSG00000123810	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000177191	Chromatin interaction
ENSG00000105341	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	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10413735	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10416743	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10417997	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420556	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10422783	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10422956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10432268	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1043413	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1077856	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10853751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083618	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083619	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11667848	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11667908	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11668924	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11670583	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670668	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670725	0.91[EUR][1000 genomes]
rs11670757	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11880539	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11883104	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12602	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12709849	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12980966	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12982607	0.83[ASN][1000 genomes]
rs13344547	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13344563	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13345590	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13346603	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1473248	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs166925	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16975238	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17318596	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17318666	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1967333	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967334	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2231940	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2241706	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241707	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241708	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241709	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241710	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241711	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288871	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304242	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2317131	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2569400	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2569754	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284648	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284649	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284650	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284651	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs284652	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs284654	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs284655	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs284656	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs284657	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284658	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284660	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284661	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284662	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284663	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3213860	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3213861	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745290	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3745292	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3786553	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3810174	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816037	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826713	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4605279	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4674	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802116	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802117	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802118	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803461	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803462	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803463	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803465	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803467	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803468	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803469	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55986560	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58961854	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62117461	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62117462	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508977	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7247332	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255918	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7258973	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8103531	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8105450	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8105833	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs878082	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs878083	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs892044	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9304593	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10417311	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	chr19:41883200-41902600	Weak transcription	Right Atrium	heart
3	chr19:41883200-41902800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:41883200-41902800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:41884600-41902400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:41886400-41902800	Weak transcription	NHDF-Ad	bronchial
7	chr19:41896600-41902600	Weak transcription	Small Intestine	intestine
8	chr19:41896800-41902400	Weak transcription	HUVEC	blood vessel
9	chr19:41897400-41902400	Weak transcription	Fetal Lung	lung
10	chr19:41897600-41902400	Weak transcription	Psoas Muscle	Psoas
11	chr19:41897600-41902600	Weak transcription	HSMMtube	muscle
12	chr19:41897800-41902200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr19:41897800-41902400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:41897800-41902400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:41897800-41902400	Weak transcription	Fetal Kidney	kidney
16	chr19:41897800-41902800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:41898000-41902200	Weak transcription	HSMM	muscle
18	chr19:41898000-41902400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:41898000-41902400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr19:41898000-41902400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr19:41898000-41902400	Weak transcription	HMEC	breast
22	chr19:41898000-41902800	Weak transcription	Colon Smooth Muscle	Colon
23	chr19:41898000-41902800	Weak transcription	NHLF	lung
24	chr19:41898200-41902200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr19:41898200-41902200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:41898200-41902200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:41898200-41902400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:41898200-41902400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:41898200-41902400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:41898200-41902400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:41898200-41902400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:41898200-41902400	Weak transcription	Brain Substantia Nigra	brain
33	chr19:41898200-41902400	Weak transcription	Colonic Mucosa	Colon
34	chr19:41898200-41902400	Weak transcription	Fetal Intestine Large	intestine
35	chr19:41898200-41902400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:41898200-41902400	Weak transcription	Osteobl	bone
37	chr19:41898200-41902600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr19:41898200-41902600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:41898200-41902800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:41898200-41902800	Weak transcription	Aorta	Aorta
41	chr19:41898200-41902800	Weak transcription	Left Ventricle	heart
42	chr19:41898200-41902800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:41898400-41902400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:41898400-41902600	Weak transcription	Esophagus	oesophagus
45	chr19:41898400-41902800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:41898800-41902400	Weak transcription	Ovary	ovary
47	chr19:41899000-41902400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:41899000-41902400	Weak transcription	Right Ventricle	heart
49	chr19:41899000-41902600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:41899200-41902400	Weak transcription	Fetal Brain Female	brain

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