Variant report

Variant	rs28529139
Chromosome Location	chr19:40967267-40967268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr19:40967218-40968143	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:40966956-40967944	K562	blood:	n/a	n/a
3	POLR2A	chr19:40967006-40967406	K562	blood:	n/a	n/a
4	POLR2A	chr19:40967009-40967464	K562	blood:	n/a	n/a
5	POLR2A	chr19:40966992-40967421	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40960093..40961977-chr19:40966563..40969268,2	MCF-7	breast:
2	chr19:40966575..40969152-chr19:41034441..41036633,2	MCF-7	breast:
3	chr19:40948595..40953789-chr19:40967165..40973013,15	MCF-7	breast:
4	chr19:40954900..40957059-chr19:40966584..40968618,2	K562	blood:
5	chr19:40945484..40955522-chr19:40966442..40973559,31	MCF-7	breast:
6	chr19:40965953..40968084-chr19:40969932..40972844,2	K562	blood:
7	chr19:40954900..40958159-chr19:40966581..40968618,3	K562	blood:
8	chr19:40962431..40968148-chr19:40968863..40972815,11	K562	blood:
9	chr19:40947599..40953337-chr19:40966407..40973377,15	K562	blood:

No data

Variant related genes	Relation type
BLVRB	TF binding region
SPTBN4	TF binding region
ENSG00000167565	Chromatin interaction
ENSG00000160460	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000090013	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10422945	1.00[TSI][hapmap]
rs11878466	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13345497	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4150995	1.00[TSI][hapmap]
rs56307925	1.00[EUR][1000 genomes]
rs7256097	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73559683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9676315	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
5	nsv911709	chr19:40928944-41060616	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv911710	chr19:40954062-40978869	Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv911711	chr19:40954062-40985003	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv911712	chr19:40957734-40978869	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv911713	chr19:40957734-40981198	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28529139	XIST	trans	lymphoblastoid	seeQTL
rs28529139	RPS4Y1	trans	lymphoblastoid	seeQTL
rs28529139	DDX3Y	trans	lymphoblastoid	seeQTL
rs28529139	KDM5D	trans	lymphoblastoid	seeQTL
rs28529139	CYorf15B	trans	lymphoblastoid	seeQTL
rs28529139	KDM6A	trans	lymphoblastoid	seeQTL
rs28529139	PNPLA4	trans	lymphoblastoid	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40951000-40970200	Weak transcription	Small Intestine	intestine
2	chr19:40951000-40970400	Weak transcription	Fetal Heart	heart
3	chr19:40951000-40970600	Weak transcription	Psoas Muscle	Psoas
4	chr19:40951000-40971200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:40951200-40969000	Weak transcription	NHDF-Ad	bronchial
6	chr19:40951200-40969800	Weak transcription	Right Atrium	heart
7	chr19:40951200-40970400	Weak transcription	Brain Angular Gyrus	brain
8	chr19:40951200-40970400	Weak transcription	Brain Substantia Nigra	brain
9	chr19:40951200-40970400	Weak transcription	HSMMtube	muscle
10	chr19:40951200-40970400	Weak transcription	NH-A	brain
11	chr19:40951200-40970600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:40951200-40970600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:40952000-40969000	Weak transcription	Osteobl	bone
14	chr19:40952000-40970000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:40952000-40970400	Weak transcription	NHLF	lung
16	chr19:40952200-40970800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:40952400-40970600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:40952400-40970600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:40952600-40970600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr19:40954200-40969000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:40954200-40970400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:40954400-40967800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:40954400-40969800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:40954400-40970400	Weak transcription	Brain Hippocampus Middle	brain
25	chr19:40954400-40970400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr19:40954800-40970200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:40954800-40970400	Weak transcription	Aorta	Aorta
28	chr19:40954800-40970400	Weak transcription	Brain Anterior Caudate	brain
29	chr19:40955000-40970600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:40955200-40970400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:40957000-40970600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr19:40957400-40970400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:40957400-40970400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr19:40957400-40970400	Weak transcription	Fetal Lung	lung
35	chr19:40960200-40969000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:40961600-40970200	Weak transcription	Fetal Muscle Leg	muscle
37	chr19:40961800-40967600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:40961800-40967800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr19:40963400-40969000	Weak transcription	NHEK	skin
40	chr19:40963600-40970400	Weak transcription	Colon Smooth Muscle	Colon
41	chr19:40964000-40969000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:40964000-40969000	Weak transcription	Hela-S3	cervix
43	chr19:40964000-40970200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:40964000-40970400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr19:40964200-40967800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr19:40964200-40970000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:40964200-40970200	Weak transcription	Left Ventricle	heart
48	chr19:40964600-40967800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr19:40964600-40967800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr19:40964600-40967800	Weak transcription	Spleen	Spleen

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