Variant report

Variant	rs1197547
Chromosome Location	chr15:42905340-42905341
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42896121..42899358-chr15:42903521..42907141,3	K562	blood:
2	chr15:42896121..42899358-chr15:42902188..42907141,4	K562	blood:
3	chr15:42903747..42906321-chr15:42930784..42933299,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10851411	0.82[MKK][hapmap]
rs11070374	0.88[CHB][hapmap]
rs11631193	0.84[ASN][1000 genomes]
rs11632169	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1197546	0.99[ASN][1000 genomes]
rs1211642	0.93[ASN][1000 genomes]
rs12903416	0.86[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1667493	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1705360	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1814518	0.92[ASN][1000 genomes]
rs2241998	0.88[CHB][hapmap];0.84[CHD][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs2595940	0.84[MKK][hapmap]
rs2617236	0.84[MKK][hapmap]
rs4447398	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4923949	0.88[ASN][1000 genomes]
rs565298	0.88[ASN][1000 genomes]
rs6493053	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6493054	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7168835	0.87[CEU][hapmap];0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs876992	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs9302112	0.84[MKK][hapmap]
rs9783683	0.87[CEU][hapmap];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1197547	SNAP23	cis	parietal	SCAN
rs1197547	MAP1A	cis	parietal	SCAN
rs1197547	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs1197547	HAUS2	cis	Liver	GTEx
rs1197547	RINT1	trans	cerebellum	SCAN
rs1197547	CEP27	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42874800-42929800	Weak transcription	Fetal Brain Female	brain
2	chr15:42877200-42911200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr15:42888800-42909600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:42888800-42911000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:42895000-42911800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:42895200-42914200	Weak transcription	HepG2	liver
7	chr15:42895200-42920800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:42897800-42914600	Weak transcription	Brain Germinal Matrix	brain
9	chr15:42897800-42930200	Weak transcription	HSMM	muscle
10	chr15:42898000-42967800	Weak transcription	Fetal Intestine Small	intestine
11	chr15:42898400-42932800	Weak transcription	Esophagus	oesophagus
12	chr15:42898600-42909800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:42898600-42929800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:42900600-42909600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:42900600-42909600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:42900600-42928000	Weak transcription	Placenta	Placenta
17	chr15:42900600-42930000	Weak transcription	HMEC	breast
18	chr15:42900800-42910000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:42900800-42914600	Weak transcription	HUVEC	blood vessel
20	chr15:42900800-42929800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr15:42901000-42921200	Weak transcription	NHDF-Ad	bronchial
22	chr15:42901000-42927800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:42901200-42909600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:42901400-42905800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:42901400-42911800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:42901400-42928400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:42901400-42929800	Weak transcription	Brain Angular Gyrus	brain
28	chr15:42901600-42905600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:42901600-42906400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:42901600-42927800	Weak transcription	Adipose Nuclei	Adipose
31	chr15:42901600-42930000	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:42901600-42930400	Weak transcription	Primary B cells from cord blood	blood
33	chr15:42901800-42910000	Weak transcription	Fetal Muscle Leg	muscle
34	chr15:42902000-42912000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:42902200-42913000	Weak transcription	Lung	lung
36	chr15:42902400-42905600	Enhancers	K562	blood
37	chr15:42902600-42908600	Weak transcription	Right Atrium	heart
38	chr15:42903200-42909600	Weak transcription	Fetal Stomach	stomach
39	chr15:42903200-42931000	Weak transcription	Fetal Intestine Large	intestine
40	chr15:42903400-42908200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:42904000-42908000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:42904000-42908000	Weak transcription	Fetal Heart	heart
43	chr15:42904000-42909600	Weak transcription	Ovary	ovary
44	chr15:42904000-42909800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr15:42904000-42930200	Weak transcription	Right Ventricle	heart
46	chr15:42904200-42929800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:42904400-42905800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:42904400-42921200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr15:42904600-42908400	Weak transcription	Colon Smooth Muscle	Colon
50	chr15:42904600-42909600	Weak transcription	Left Ventricle	heart

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