Variant report

Variant	rs27852
Chromosome Location	chr5:96046039-96046040
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96044782..96047336-chr5:96048549..96051619,3	K562	blood:
2	chr5:96045462..96047698-chr5:96048797..96050633,2	MCF-7	breast:
3	chr5:96037082..96041395-chr5:96043344..96047377,11	K562	blood:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs149313	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs149319	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs151828	0.86[ASN][1000 genomes]
rs151829	0.83[ASN][1000 genomes]
rs152014	0.93[YRI][hapmap]
rs152020	0.92[YRI][hapmap]
rs26483	0.93[YRI][hapmap]
rs26515	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs697976	0.86[ASN][1000 genomes]
rs9314177	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs27852	CAST	cis	parietal	SCAN
rs27852	C5orf36	cis	cerebellum	SCAN
rs27852	CAST	cis	cerebellum	SCAN
rs27852	CTC-506B8.1	cis	Whole Blood	GTEx
rs27852	SPTBN5	trans	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96039200-96050600	Weak transcription	Gastric	stomach
2	chr5:96039200-96054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:96039200-96054400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:96039200-96054400	Weak transcription	Spleen	Spleen
5	chr5:96039200-96059800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:96039400-96050200	Weak transcription	Aorta	Aorta
7	chr5:96039600-96046200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr5:96039600-96063600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:96039800-96048000	Weak transcription	Pancreas	Pancrea
10	chr5:96039800-96049600	Weak transcription	Fetal Muscle Leg	muscle
11	chr5:96039800-96049800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:96040000-96046600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:96040000-96047400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:96040000-96049600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:96040000-96049800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:96040000-96050000	Weak transcription	Primary T cells from cord blood	blood
17	chr5:96040000-96050000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:96040000-96050200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr5:96040000-96050400	Weak transcription	Primary B cells from cord blood	blood
20	chr5:96040000-96054400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:96040000-96054400	Weak transcription	Fetal Stomach	stomach
22	chr5:96040200-96046600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:96040200-96046800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:96040200-96049400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:96040200-96049800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:96040200-96050200	Weak transcription	Brain Substantia Nigra	brain
27	chr5:96040200-96050600	Weak transcription	Brain Anterior Caudate	brain
28	chr5:96040400-96047200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:96040400-96049800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr5:96040600-96046800	Weak transcription	Liver	Liver
31	chr5:96040600-96047400	Weak transcription	Brain Hippocampus Middle	brain
32	chr5:96040600-96048600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr5:96040600-96050200	Weak transcription	Fetal Kidney	kidney
34	chr5:96041000-96046800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:96041000-96048600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:96041600-96046200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:96041600-96054600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr5:96041800-96049600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr5:96042600-96046600	Weak transcription	HepG2	liver
40	chr5:96042800-96076200	Weak transcription	GM12878-XiMat	blood
41	chr5:96043200-96046400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr5:96043600-96054400	Weak transcription	Esophagus	oesophagus
43	chr5:96044200-96046200	Enhancers	HMEC	breast
44	chr5:96044200-96046400	Enhancers	Psoas Muscle	Psoas
45	chr5:96044400-96048000	Weak transcription	Lung	lung
46	chr5:96044400-96049600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:96044600-96046200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:96044600-96046200	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr5:96044800-96047800	Weak transcription	Small Intestine	intestine
50	chr5:96044800-96050200	Weak transcription	Primary monocytes fromperipheralblood	blood

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