Variant report

Variant	rs1955915
Chromosome Location	chr14:24838621-24838622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr14:24837851-24838627	GM12878	blood:	n/a	n/a
2	POLR2A	chr14:24835171-24838793	SK-N-MC	brain:	n/a	n/a
3	CHD1	chr14:24834050-24838822	IMR90	lung:	n/a	chr14:24835865-24835875
4	STAT5A	chr14:24838029-24838765	GM12878	blood:	n/a	chr14:24838667-24838679 chr14:24838060-24838072 chr14:24838062-24838074
5	SIN3A	chr14:24834876-24838748	H1-hESC	embryonic stem cell:	n/a	chr14:24837936-24837945 chr14:24837973-24837982 chr14:24836086-24836099 chr14:24835902-24835915
6	ZBTB7A	chr14:24835684-24838645	ECC-1	luminal epithelium:	n/a	chr14:24837803-24837811 chr14:24836772-24836786 chr14:24838030-24838039
7	POLR2A	chr14:24837708-24838637	ProgFib	skin:	n/a	n/a
8	MAZ	chr14:24834812-24838705	IMR90	lung:	n/a	chr14:24837432-24837442 chr14:24837797-24837807 chr14:24835199-24835209 chr14:24837336-24837346 chr14:24837503-24837513
9	GATA2	chr14:24838049-24838721	SH-SY5Y	brain:	n/a	n/a
10	MXI1	chr14:24834918-24838667	IMR90	lung:	n/a	chr14:24838289-24838304

No.	Distal block	Cell Line	Cell type
1	chr14:24837984..24840011-chr14:24867757..24869920,2	K562	blood:
2	chr14:24833553..24839988-chr14:24894553..24902357,9	K562	blood:
3	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
4	chr14:24836714..24839783-chr14:24910555..24913487,3	K562	blood:
5	chr14:24796879..24804920-chr14:24831628..24840088,12	MCF-7	breast:
6	chr14:24836675..24839120-chr14:24840231..24842410,2	K562	blood:
7	chr14:24816528..24849574-chr14:24893305..24914155,145	MCF-7	breast:
8	chr14:24837386..24841607-chr14:24843315..24846573,5	K562	blood:
9	chr14:24833867..24840783-chr14:24879585..24886299,12	MCF-7	breast:
10	chr14:24833707..24839988-chr14:24896546..24902736,10	K562	blood:

Variant related genes	Relation type
NFATC4	TF binding region
ENSG00000205978	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000100445	Chromatin interaction
ENSG00000139899	Chromatin interaction
ENSG00000129467	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10131172	0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2144490	0.81[YRI][hapmap]
rs2332327	0.81[YRI][hapmap]
rs57193392	0.97[ASN][1000 genomes]
rs6573766	0.91[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs9788516	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1955915	NFATC4	cis	cerebellum	SCAN
rs1955915	NYNRIN	cis	cerebellum	SCAN
rs1955915	DHRS1	cis	cerebellum	SCAN
rs1955915	OR6S1	cis	cerebellum	SCAN
rs1955915	ADCY4	cis	cerebellum	SCAN
rs1955915	ADCY4	cis	multi-tissue	Pritchard
rs1955915	RNASE11	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24834800-24838800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr14:24835000-24838800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr14:24835000-24838800	Active TSS	Fetal Kidney	kidney
4	chr14:24835200-24839200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr14:24837000-24838800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
6	chr14:24837000-24838800	Active TSS	Rectal Smooth Muscle	rectum
7	chr14:24837000-24839000	Active TSS	Right Ventricle	heart
8	chr14:24837600-24838800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr14:24837800-24839800	Enhancers	Fetal Brain Male	brain
10	chr14:24838000-24838800	Flanking Active TSS	Pancreas	Pancrea
11	chr14:24838000-24838800	Bivalent Enhancer	Stomach Mucosa	stomach
12	chr14:24838000-24838800	Flanking Active TSS	NH-A	brain
13	chr14:24838000-24839000	Bivalent/Poised TSS	HepG2	liver
14	chr14:24838200-24838800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
15	chr14:24838200-24838800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr14:24838200-24838800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr14:24838200-24838800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr14:24838200-24838800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr14:24838200-24838800	Active TSS	Adipose Nuclei	Adipose
20	chr14:24838200-24838800	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr14:24838200-24838800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
22	chr14:24838200-24838800	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
23	chr14:24838200-24839400	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr14:24838200-24850200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr14:24838400-24838800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr14:24838400-24838800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr14:24838400-24838800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr14:24838400-24838800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr14:24838400-24838800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr14:24838400-24838800	Flanking Active TSS	Fetal Brain Female	brain
31	chr14:24838400-24838800	Flanking Active TSS	Left Ventricle	heart
32	chr14:24838400-24838800	Flanking Active TSS	NHDF-Ad	bronchial
33	chr14:24838400-24838800	Transcr. at gene 5' and 3'	NHLF	lung
34	chr14:24838400-24839000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr14:24838400-24839000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr14:24838400-24839200	Transcr. at gene 5' and 3'	Osteobl	bone
37	chr14:24838400-24839600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr14:24838400-24839600	Enhancers	Lung	lung
39	chr14:24838400-24843000	Weak transcription	Aorta	Aorta
40	chr14:24838400-24844400	Weak transcription	Esophagus	oesophagus
41	chr14:24838600-24838800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr14:24838600-24838800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:24838600-24838800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:24838600-24838800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr14:24838600-24838800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr14:24838600-24838800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr14:24838600-24838800	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr14:24838600-24838800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr14:24838600-24838800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr14:24838600-24838800	Enhancers	Muscle Satellite Cultured Cells	--

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