Variant report

Variant	rs6816370
Chromosome Location	chr4:103939433-103939434
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:103939290..103941990-chr4:103997804..104000978,3	K562	blood:
2	chr4:103747527..103750862-chr4:103937830..103941231,4	MCF-7	breast:
3	chr4:103934937..103936463-chr4:103938822..103940719,2	MCF-7	breast:
4	chr4:103937535..103939748-chr4:103948954..103951628,2	MCF-7	breast:
5	chr4:103748747..103750946-chr4:103939260..103942064,3	MCF-7	breast:
6	chr4:103939297..103941618-chr4:103997332..103999799,2	K562	blood:
7	chr4:103747151..103749001-chr4:103938007..103939822,2	K562	blood:
8	chr4:103421990..103423686-chr4:103938282..103940885,2	MCF-7	breast:
9	chr4:103772094..103774668-chr4:103939126..103940679,2	MCF-7	breast:
10	chr4:103929312..103930892-chr4:103937396..103939916,2	MCF-7	breast:
11	chr4:103421593..103424113-chr4:103937527..103940611,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260651	Chromatin interaction
ENSG00000164038	Chromatin interaction
ENSG00000109320	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000246560	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10006474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10013062	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10516495	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10516496	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11929841	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11946020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13113099	0.85[JPT][hapmap]
rs13149311	0.80[JPT][hapmap];0.83[AMR][1000 genomes]
rs13150953	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13151569	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1481279	0.86[JPT][hapmap]
rs223317	0.96[CEU][hapmap]
rs223331	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs223361	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs223366	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs223374	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2866416	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34475639	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698876	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699048	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533039	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6843738	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]
rs7437975	0.81[ASN][1000 genomes]
rs7665026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7691873	0.86[JPT][hapmap]
rs9991335	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv461598	chr4:103807720-103953389	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv594978	chr4:103807720-103953389	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv879684	chr4:103887561-103939894	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6816370	KRT8P46	cis	lung	GTEx
rs6816370	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs6816370	MANBA	cis	multi-tissue	Pritchard
rs6816370	LRRC37A15P	cis	Thyroid	GTEx
rs6816370	MANBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103932600-103939600	Weak transcription	HepG2	liver
2	chr4:103933000-103939600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:103933000-103940000	Weak transcription	Right Atrium	heart
4	chr4:103933200-103939800	Weak transcription	NHLF	lung
5	chr4:103933200-103940400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:103933600-103939800	Weak transcription	NHDF-Ad	bronchial
7	chr4:103934000-103939800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:103934000-103939800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:103934000-103939800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:103934000-103939800	Weak transcription	Psoas Muscle	Psoas
11	chr4:103934000-103939800	Weak transcription	NHEK	skin
12	chr4:103934200-103939600	Weak transcription	K562	blood
13	chr4:103934200-103939800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:103934200-103939800	Weak transcription	Adipose Nuclei	Adipose
15	chr4:103934200-103939800	Weak transcription	Brain Substantia Nigra	brain
16	chr4:103934200-103939800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:103934200-103940200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:103934400-103939600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:103934400-103940000	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:103934600-103939800	Weak transcription	Brain Anterior Caudate	brain
21	chr4:103936800-103940200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:103938400-103939800	Enhancers	Hela-S3	cervix
23	chr4:103938800-103939800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:103939000-103939800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:103939000-103939800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:103939000-103939800	Weak transcription	Fetal Intestine Large	intestine
27	chr4:103939000-103939800	Weak transcription	Fetal Kidney	kidney
28	chr4:103939000-103939800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:103939000-103940000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr4:103939200-103939800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr4:103939200-103939800	Enhancers	GM12878-XiMat	blood
32	chr4:103939400-103940000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:103939400-103940000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr4:103939400-103940200	Enhancers	Primary B cells from peripheral blood	blood

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