Variant report

Variant	rs16883571
Chromosome Location	chr6:74019338-74019339
allele	A/G
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:3)
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
1	chr6:74018617..74020402-chr6:74229038..74231578,2	K562	blood:
2	chr6:74017993..74019830-chr6:74023707..74026183,2	K562	blood:
3	chr6:74019135..74019848-chr8:134309134..134310019,2	HCT-116	colon:
4	chr6:74019132..74021037-chr6:74035102..74038001,2	MCF-7	breast:
5	chr6:74019175..74020751-chr6:74101665..74105754,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KHDC1-1	chr6:74019275-74019866	NONHSAT113546
2	lnc-KHDC1-1	chr6:74019275-74019451	NONHSAT113544
3	lnc-KHDC1-1	chr6:74019275-74019451	NONHSAT113547

No data

Variant related genes	Relation type
ENSG00000104419	Chromatin interaction
ENSG00000203907	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000226840	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000080007	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10455272	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943084	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943085	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943088	0.85[MEX][hapmap];0.81[EUR][1000 genomes]
rs11963438	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190274	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191242	1.00[JPT][hapmap]
rs12198600	1.00[JPT][hapmap]
rs12199709	1.00[ASN][1000 genomes]
rs12199821	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203786	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207480	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208950	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210588	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213765	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215980	1.00[JPT][hapmap]
rs12216244	0.85[MEX][hapmap];0.81[EUR][1000 genomes]
rs12529651	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883518	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883564	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35542640	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45491600	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55810380	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159527	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411447	0.93[EUR][1000 genomes]
rs62411451	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438240	0.81[EUR][1000 genomes]
rs62438242	0.81[EUR][1000 genomes]
rs62438243	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438245	1.00[ASN][1000 genomes]
rs62440564	0.83[ASN][1000 genomes]
rs62440565	0.83[ASN][1000 genomes]
rs72947904	1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16883571	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx
rs16883571	C6orf148	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74016200-74020400	Active TSS	Hela-S3	cervix
2	chr6:74017200-74020800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:74018200-74020400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:74018200-74020600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr6:74018400-74019800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:74018400-74020200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:74018400-74020400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:74018400-74020400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:74018400-74020400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr6:74018400-74020600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:74018400-74020600	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr6:74018400-74020600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:74018600-74019600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:74018600-74019800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:74018600-74019800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:74018600-74020200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:74018600-74020200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:74018600-74020200	Active TSS	GM12878-XiMat	blood
19	chr6:74018600-74020400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr6:74018600-74020400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:74018600-74020400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr6:74018600-74020400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr6:74018600-74020400	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr6:74018600-74020400	Flanking Active TSS	Fetal Thymus	thymus
25	chr6:74018600-74020400	Active TSS	A549	lung
26	chr6:74018600-74020600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:74018600-74020600	Active TSS	Brain Germinal Matrix	brain
28	chr6:74018600-74020600	Active TSS	Fetal Brain Female	brain
29	chr6:74018800-74019400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:74018800-74019400	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr6:74018800-74019400	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr6:74018800-74019400	Flanking Active TSS	Thymus	Thymus
33	chr6:74018800-74019600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
34	chr6:74018800-74019600	Flanking Active TSS	NH-A	brain
35	chr6:74018800-74019800	Flanking Active TSS	HUVEC	blood vessel
36	chr6:74018800-74020000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr6:74018800-74020000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
38	chr6:74018800-74020200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:74018800-74020200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:74018800-74020200	Flanking Active TSS	HMEC	breast
41	chr6:74018800-74020400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:74018800-74020400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:74018800-74020400	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr6:74018800-74020400	Active TSS	NHDF-Ad	bronchial
45	chr6:74018800-74020400	Active TSS	NHLF	lung
46	chr6:74018800-74020600	Active TSS	Brain Angular Gyrus	brain
47	chr6:74018800-74020600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:74018800-74020600	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr6:74019000-74019400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:74019000-74019400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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