Variant report

Variant	rs1950770
Chromosome Location	chr14:35345352-35345353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr14:35342089-35345455	SK-N-SH	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:35341948..35345853-chr14:35449382..35453241,7	K562	blood:
2	chr14:35341867..35346512-chr14:35447191..35456965,26	MCF-7	breast:
3	chr14:35345148..35348932-chr14:35351443..35354941,5	K562	blood:
4	chr14:35341203..35346354-chr14:35872500..35877183,6	MCF-7	breast:
5	chr14:35342567..35345567-chr14:35590904..35592504,3	MCF-7	breast:
6	chr14:35343897..35345985-chr7:127725161..127726681,2	MCF-7	breast:
7	chr14:35343382..35345457-chr14:35494554..35496991,2	MCF-7	breast:
8	chr14:35327682..35333013-chr14:35342164..35345913,7	MCF-7	breast:
9	chr14:35341954..35346847-chr14:35449484..35456301,15	MCF-7	breast:
10	chr14:35342612..35346213-chr14:35514260..35516898,3	K562	blood:
11	chr14:35341141..35345954-chr14:35450498..35453739,11	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRP54-1	chr14:35343549-35345665	ENSG00000258738.1

No data

Variant related genes	Relation type
BAZ1A	TF binding region
ENSG00000151327	Chromatin interaction
ENSG00000100906	Chromatin interaction
ENSG00000100883	Chromatin interaction
ENSG00000198604	Chromatin interaction
ENSG00000258790	Chromatin interaction
ENSG00000197157	Chromatin interaction
ENSG00000258704	Chromatin interaction
ENSG00000092020	Chromatin interaction
ENSG00000100890	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10129577	0.87[YRI][hapmap]
rs10133537	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11156864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11623145	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200413	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1200415	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1741205	0.83[CEU][hapmap]
rs2145031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28628142	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28686888	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7148005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[ASN][1000 genomes]
rs7148739	0.88[YRI][hapmap]
rs799672	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs799676	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392700	chr14:34989406-35365530	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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	85 gene(s)	inside rSNPs	diseases
2	nsv1041857	chr14:35084889-35417180	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1052162	chr14:35245349-35451187	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1053722	chr14:35257458-35465784	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv1045939	chr14:35311074-35494703	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv456203	chr14:35311272-35512335	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv564200	chr14:35311272-35512335	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
8	esv3361541	chr14:35342726-35345574	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1950770	KIAA0391	cis	parietal	SCAN
rs1950770	SRP54	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35341400-35345400	Active TSS	GM12878-XiMat	blood
2	chr14:35341600-35345400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr14:35342600-35345600	Active TSS	K562	blood
4	chr14:35343800-35345400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr14:35344600-35345400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr14:35344600-35345400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr14:35344800-35345400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr14:35344800-35345400	Flanking Active TSS	Dnd41	blood
9	chr14:35344800-35345400	Flanking Active TSS	HepG2	liver
10	chr14:35344800-35345400	Flanking Active TSS	HUVEC	blood vessel
11	chr14:35344800-35345400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr14:35344800-35345400	Flanking Active TSS	Osteobl	bone
13	chr14:35344800-35347000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr14:35345000-35345400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr14:35345000-35345400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr14:35345000-35345400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr14:35345000-35345400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr14:35345000-35345400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr14:35345000-35345400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr14:35345000-35345400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:35345000-35345400	Enhancers	Liver	Liver
22	chr14:35345000-35345400	Enhancers	Fetal Kidney	kidney
23	chr14:35345000-35345400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr14:35345000-35345400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr14:35345000-35345400	Flanking Active TSS	NHLF	lung
26	chr14:35345000-35345600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr14:35345000-35345600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr14:35345000-35345600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr14:35345000-35345600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr14:35345000-35345800	Enhancers	Stomach Mucosa	stomach
31	chr14:35345200-35345400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:35345200-35345400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr14:35345200-35345400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
34	chr14:35345200-35345400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr14:35345200-35345400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr14:35345200-35345400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr14:35345200-35345400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr14:35345200-35345400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr14:35345200-35345400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr14:35345200-35345400	Enhancers	Adipose Nuclei	Adipose
41	chr14:35345200-35345400	Enhancers	Brain Germinal Matrix	brain
42	chr14:35345200-35345400	Enhancers	Brain Hippocampus Middle	brain
43	chr14:35345200-35345400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr14:35345200-35345400	Flanking Active TSS	Colon Smooth Muscle	Colon
45	chr14:35345200-35345400	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr14:35345200-35345400	Enhancers	Fetal Heart	heart
47	chr14:35345200-35345400	Enhancers	Fetal Intestine Large	intestine
48	chr14:35345200-35345400	Enhancers	Fetal Lung	lung
49	chr14:35345200-35345400	Flanking Active TSS	HMEC	breast
50	chr14:35345200-35345400	Enhancers	NH-A	brain

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