Variant report

Variant	rs10455092
Chromosome Location	chr6:74001064-74001065
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	6:73927031-73938730..6:74000304-74012200	K562	blood:
2	6:74000304-74012200..6:74062967-74076046	GM12878	blood:
3	6:74000304-74012200..6:74160392-74184826	K562	blood:
4	6:74000304-74012200..6:74078047-74099067	H1-hESC	embryonic stem cell:	embryo
5	6:74000304-74012200..6:74099986-74112890	H1-hESC	embryonic stem cell:	embryo

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf221-2	chr6:74000256-74001137	NONHSAT113543
2	lnc-C6orf221-2	chr6:74000256-74001426	NONHSAT113548

No data

Variant related genes	Relation type
ENSG00000235174	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000135297	Chromatin interaction
ENSG00000203908	Chromatin interaction
ENSG00000207023	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000203909	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000224221	Chromatin interaction
ENSG00000231332	Chromatin interaction
ENSG00000256980	Chromatin interaction
ENSG00000203907	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10455273	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10455274	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1066687	0.93[ASN][1000 genomes]
rs12153835	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12203663	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208781	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12210531	0.94[ASN][1000 genomes]
rs12216162	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[ASN][1000 genomes]
rs12526643	0.93[ASN][1000 genomes]
rs12529624	0.96[ASN][1000 genomes]
rs12529658	0.96[ASN][1000 genomes]
rs12530029	0.92[ASN][1000 genomes]
rs12530079	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13194683	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13212903	0.96[ASN][1000 genomes]
rs13213885	0.96[ASN][1000 genomes]
rs13219250	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1555443	0.96[ASN][1000 genomes]
rs1869559	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1970551	0.96[ASN][1000 genomes]
rs1974368	0.94[ASN][1000 genomes]
rs2124004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2124006	0.84[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap]
rs2168113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254630	0.96[ASN][1000 genomes]
rs2603471	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2603472	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2603473	0.91[EUR][1000 genomes]
rs2603474	0.82[EUR][1000 genomes]
rs2797086	0.93[ASN][1000 genomes]
rs28530192	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2984129	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34246858	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34531450	0.96[ASN][1000 genomes]
rs34637067	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34821383	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35664677	0.94[ASN][1000 genomes]
rs4706533	0.92[ASN][1000 genomes]
rs4706534	0.92[ASN][1000 genomes]
rs4708041	0.92[ASN][1000 genomes]
rs4708042	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs471270	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs471938	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502107	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs502282	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs509406	0.96[ASN][1000 genomes]
rs510551	0.91[ASN][1000 genomes]
rs511219	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs512366	0.91[ASN][1000 genomes]
rs555779	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57113415	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs573535	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576229	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579736	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61493410	0.89[ASN][1000 genomes]
rs62438232	0.96[ASN][1000 genomes]
rs62438233	0.96[ASN][1000 genomes]
rs62438235	0.96[ASN][1000 genomes]
rs62438239	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66984567	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915004	0.90[EUR][1000 genomes]
rs6923111	0.88[ASN][1000 genomes]
rs6923734	0.95[ASN][1000 genomes]
rs7382700	0.91[ASN][1000 genomes]
rs7740081	0.92[ASN][1000 genomes]
rs7742847	0.96[ASN][1000 genomes]
rs7743609	0.96[ASN][1000 genomes]
rs7744174	0.92[ASN][1000 genomes]
rs7753960	0.80[GIH][hapmap]
rs7758047	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759043	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7764719	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7765618	0.96[ASN][1000 genomes]
rs7769905	1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap];0.94[ASN][1000 genomes]
rs7773619	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9800483	0.85[ASN][1000 genomes]
rs9800824	0.94[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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv970143	chr6:73998606-74001817	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10455092	RP11-398K22.12	cis	Skin Sun Exposed Lower leg	GTEx
rs10455092	QPCT	trans	cerebellum	SCAN
rs10455092	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10455092	KHDC1	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73973600-74018600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:73973600-74018600	Weak transcription	A549	lung
3	chr6:73973600-74018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:73974000-74009000	Weak transcription	HSMM	muscle
5	chr6:73974000-74018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:73974400-74008800	Weak transcription	NH-A	brain
7	chr6:73974400-74009400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:73974600-74008600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:73974800-74008600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:73977400-74008800	Weak transcription	Fetal Brain Male	brain
11	chr6:73979200-74004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:73983800-74018600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:73984400-74018600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:73984600-74002200	Weak transcription	Primary T cells from cord blood	blood
15	chr6:73984800-74004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:73984800-74008600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:73985200-74004600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:73985200-74008800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:73985400-74009000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:73985600-74004800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:73985600-74008800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:73985600-74008800	Weak transcription	Thymus	Thymus
23	chr6:73985800-74006800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:73985800-74008800	Weak transcription	Ovary	ovary
25	chr6:73986400-74008600	Weak transcription	Fetal Brain Female	brain
26	chr6:73989000-74017200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:73989800-74008800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:73990000-74003800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:73991600-74002600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:73992400-74013200	Weak transcription	GM12878-XiMat	blood
31	chr6:73994200-74018600	Weak transcription	Stomach Mucosa	stomach
32	chr6:73995200-74002800	Strong transcription	Dnd41	blood
33	chr6:73996000-74008600	Weak transcription	Fetal Heart	heart
34	chr6:73996000-74008600	Weak transcription	Fetal Kidney	kidney
35	chr6:73996000-74009800	Weak transcription	K562	blood
36	chr6:73996000-74015800	Weak transcription	Hela-S3	cervix
37	chr6:73998200-74004800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:73999000-74008600	Weak transcription	Brain Substantia Nigra	brain
39	chr6:74000000-74001200	Enhancers	HUVEC	blood vessel
40	chr6:74000000-74002600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:74000200-74001800	Strong transcription	Fetal Stomach	stomach
42	chr6:74000200-74002000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:74000200-74002600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:74000400-74001400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:74000400-74001400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:74000400-74001400	Enhancers	NHDF-Ad	bronchial
47	chr6:74000400-74001600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr6:74000400-74001800	Strong transcription	Brain Germinal Matrix	brain
49	chr6:74000400-74001800	Strong transcription	Fetal Muscle Leg	muscle
50	chr6:74000400-74002000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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