Variant report

Variant	rs555779
Chromosome Location	chr6:74014468-74014469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	6:74012200-74019242..6:74078047-74099067	H1-hESC	embryonic stem cell:	embryo
2	6:74012200-74019242..6:74062967-74076046	Hela-S3	cervix:
3	chr6:74010598..74017256-chr6:74017490..74021575,10	K562	blood:

Variant related genes	Relation type
ENSG00000203908	Chromatin interaction
ENSG00000203909	Chromatin interaction
ENSG00000235174	Chromatin interaction
ENSG00000203907	Chromatin interaction
ENSG00000231332	Chromatin interaction
ENSG00000135314	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10455092	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]
rs10455273	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10455274	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1066687	0.95[ASN][1000 genomes]
rs12153835	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12203663	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12208781	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12210531	0.92[ASN][1000 genomes]
rs12216162	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12526643	0.91[ASN][1000 genomes]
rs12529624	0.94[ASN][1000 genomes]
rs12529658	0.94[ASN][1000 genomes]
rs12530029	0.91[ASN][1000 genomes]
rs12530079	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13194683	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13212903	0.94[ASN][1000 genomes]
rs13213885	0.94[ASN][1000 genomes]
rs13219250	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1555443	0.94[ASN][1000 genomes]
rs1869559	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1970551	0.94[ASN][1000 genomes]
rs1974368	0.92[ASN][1000 genomes]
rs2124004	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124006	0.84[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs2168113	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2254630	0.94[ASN][1000 genomes]
rs2603471	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2603472	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2603473	0.91[EUR][1000 genomes]
rs2603474	0.82[EUR][1000 genomes]
rs2797086	0.91[ASN][1000 genomes]
rs28530192	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2984129	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34246858	0.93[ASN][1000 genomes]
rs34531450	0.94[ASN][1000 genomes]
rs34637067	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34821383	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35664677	0.92[ASN][1000 genomes]
rs4706533	0.91[ASN][1000 genomes]
rs4706534	0.91[ASN][1000 genomes]
rs4708041	0.91[ASN][1000 genomes]
rs4708042	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs471270	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs471938	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs502107	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs502282	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs509406	0.94[ASN][1000 genomes]
rs510551	0.89[ASN][1000 genomes]
rs511219	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs512366	0.89[ASN][1000 genomes]
rs57113415	0.85[ASN][1000 genomes]
rs573535	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs576229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs579736	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61493410	0.87[ASN][1000 genomes]
rs62438232	0.94[ASN][1000 genomes]
rs62438233	0.94[ASN][1000 genomes]
rs62438235	0.94[ASN][1000 genomes]
rs62438239	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66984567	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6915004	0.92[EUR][1000 genomes]
rs6923111	0.86[ASN][1000 genomes]
rs6923734	0.93[ASN][1000 genomes]
rs7382700	0.90[ASN][1000 genomes]
rs7740081	0.91[ASN][1000 genomes]
rs7742847	0.94[ASN][1000 genomes]
rs7743609	0.94[ASN][1000 genomes]
rs7744174	0.91[ASN][1000 genomes]
rs7753960	0.92[GIH][hapmap]
rs7758047	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7759043	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7759315	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7764719	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7765618	0.94[ASN][1000 genomes]
rs7769905	1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs7773619	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9800483	0.84[ASN][1000 genomes]
rs9800824	0.92[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	nsv518874	chr6:74014468-74041424	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs555779	DDX43	cis	lymphoblastoid	seeQTL
rs555779	RP11-398K22.12	cis	Skin Sun Exposed Lower leg	GTEx
rs555779	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:55 , 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	chr6:73974000-74018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:73983800-74018600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:73984400-74018600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:73989000-74017200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:73994200-74018600	Weak transcription	Stomach Mucosa	stomach
9	chr6:73996000-74015800	Weak transcription	Hela-S3	cervix
10	chr6:74001000-74017200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:74005200-74018600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:74007800-74017400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:74008800-74018400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:74009000-74018400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:74009400-74017200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:74009400-74017200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:74009400-74017200	Weak transcription	Fetal Thymus	thymus
18	chr6:74009400-74017200	Weak transcription	Pancreas	Pancrea
19	chr6:74009400-74017400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:74009400-74018400	Weak transcription	Fetal Lung	lung
21	chr6:74009400-74019000	Weak transcription	Right Atrium	heart
22	chr6:74009600-74016000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:74009600-74016000	Weak transcription	Fetal Brain Male	brain
24	chr6:74009600-74017200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:74009600-74017400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:74009600-74017400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:74009600-74017400	Weak transcription	Osteobl	bone
28	chr6:74009600-74018600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:74009600-74018600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:74009600-74018600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:74009600-74018600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:74009600-74018600	Weak transcription	NHLF	lung
33	chr6:74009800-74015800	Weak transcription	Fetal Brain Female	brain
34	chr6:74009800-74015800	Weak transcription	Fetal Muscle Leg	muscle
35	chr6:74009800-74016600	Weak transcription	Brain Germinal Matrix	brain
36	chr6:74009800-74018800	Weak transcription	Ovary	ovary
37	chr6:74009800-74018800	Weak transcription	Spleen	Spleen
38	chr6:74010000-74016000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:74010000-74018400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr6:74010000-74018600	Weak transcription	Fetal Intestine Small	intestine
41	chr6:74010000-74018800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:74010000-74018800	Weak transcription	Thymus	Thymus
43	chr6:74010600-74016000	Weak transcription	K562	blood
44	chr6:74010600-74016200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:74010600-74018200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:74011800-74016800	Weak transcription	Fetal Stomach	stomach
47	chr6:74012400-74015800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:74012400-74017400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:74012600-74018400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:74013200-74014800	Enhancers	GM12878-XiMat	blood

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