Variant report

Variant	rs1620253
Chromosome Location	chr15:45472710-45472711
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:8)
LncRNA
region (count:0)
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	RUNX3	chr15:45472381-45472715	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45470589..45472995-chr15:45489124..45491462,3	MCF-7	breast:
2	chr15:45458776..45462841-chr15:45467209..45473486,10	K562	blood:
3	chr15:45472426..45475821-chr15:45489773..45493159,3	K562	blood:
4	chr15:45472426..45474381-chr15:45491659..45493233,2	K562	blood:
5	chr15:45471561..45475350-chr15:45693833..45697444,3	MCF-7	breast:
6	chr15:45461861..45465831-chr15:45472049..45473955,3	K562	blood:
7	chr15:45457813..45459796-chr15:45472458..45474302,2	MCF-7	breast:
8	chr15:45471595..45473672-chr15:45478332..45480462,2	MCF-7	breast:

No data

Variant related genes	Relation type
SHF	TF binding region
ENSG00000171766	Chromatin interaction
ENSG00000259539	Chromatin interaction
ENSG00000259932	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000260035	Chromatin interaction
ENSG00000259519	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1145089	1.00[JPT][hapmap]
rs1648304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648310	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648313	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706807	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706811	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706812	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706815	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1706817	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706827	0.84[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs1706829	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs2162246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292468	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs2458237	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467819	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467820	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775830	0.80[AMR][1000 genomes]
rs6493143	1.00[JPT][hapmap]
rs7169193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
6	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1620253	SHF	cis	cerebellum	SCAN
rs1620253	CCNDBP1	cis	cerebellum	SCAN
rs1620253	SHF	cis	parietal	SCAN
rs1620253	ADAL	cis	parietal	SCAN
rs1620253	FSIP1	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45459800-45478000	Weak transcription	Aorta	Aorta
2	chr15:45460000-45474800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:45460000-45477200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr15:45460000-45478600	Weak transcription	Thymus	Thymus
5	chr15:45460200-45478000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:45460400-45475200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:45460600-45475400	Weak transcription	Brain Anterior Caudate	brain
8	chr15:45460600-45475600	Weak transcription	Left Ventricle	heart
9	chr15:45460600-45478000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:45460600-45478200	Weak transcription	Adipose Nuclei	Adipose
11	chr15:45461200-45473200	Weak transcription	Fetal Brain Male	brain
12	chr15:45462200-45477200	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:45462400-45473600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr15:45462800-45473800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:45463000-45473800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:45466000-45478800	Weak transcription	Right Ventricle	heart
17	chr15:45466400-45477600	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:45466800-45473800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:45467600-45476200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:45467600-45477400	Weak transcription	Brain Angular Gyrus	brain
21	chr15:45467800-45473800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:45467800-45477400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:45468000-45477800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:45470000-45473800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:45470200-45475600	Weak transcription	Placenta	Placenta
26	chr15:45470400-45473200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:45470400-45473400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:45470400-45473600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:45470400-45474000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:45470400-45474000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:45470400-45475400	Weak transcription	Fetal Lung	lung
32	chr15:45470400-45476800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:45470600-45473400	Weak transcription	Fetal Intestine Small	intestine
34	chr15:45470600-45475200	Weak transcription	Liver	Liver
35	chr15:45470600-45475400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:45470600-45475800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:45470800-45473800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:45471200-45473800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:45471400-45473600	Enhancers	Stomach Mucosa	stomach
40	chr15:45471400-45473600	Enhancers	HMEC	breast
41	chr15:45471400-45474400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:45471400-45477000	Enhancers	HSMM	muscle
43	chr15:45471400-45477400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr15:45471600-45473200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:45471600-45474200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:45471600-45474600	Enhancers	Fetal Muscle Trunk	muscle
47	chr15:45471600-45478000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:45471800-45472800	Enhancers	Esophagus	oesophagus
49	chr15:45471800-45472800	Genic enhancers	Ovary	ovary
50	chr15:45471800-45472800	Enhancers	Rectal Mucosa Donor 31	rectum

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