Variant report

Variant	rs12549064
Chromosome Location	chr8:9442027-9442028
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:9411520..9414432-chr8:9439337..9442091,3	K562	blood:

Variant related genes	Relation type
ENSG00000173273	Chromatin interaction
ENSG00000272267	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10094343	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10104247	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11249930	0.85[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11249943	0.87[ASW][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs11784181	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs12335065	0.83[EUR][1000 genomes]
rs12542420	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12543591	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28437757	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28464158	0.83[EUR][1000 genomes]
rs28610188	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28615758	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4265191	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4427176	0.90[CEU][hapmap]
rs4457339	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4481595	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4560795	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4562329	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4573280	0.85[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4841178	0.86[EUR][1000 genomes]
rs4841180	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4841200	0.87[ASW][hapmap];0.85[CEU][hapmap];0.81[GIH][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap]
rs62491544	0.81[EUR][1000 genomes]
rs62493907	0.91[ASN][1000 genomes]
rs62493913	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6982215	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6989782	0.81[LWK][hapmap]
rs6996829	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7006406	0.85[CEU][hapmap];0.82[YRI][hapmap]
rs7464476	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7821799	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7825818	0.85[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs7829326	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7833036	0.81[EUR][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	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv497927	chr8:9097611-9544519	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12549064	TNKS	cis	parietal	SCAN
rs12549064	BLK	cis	parietal	SCAN
rs12549064	PRSS55	cis	cerebellum	SCAN
rs12549064	MFHAS1	cis	cerebellum	SCAN
rs12549064	DEFB134	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9414400-9459600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:9417200-9450000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr8:9427400-9450000	Weak transcription	Thymus	Thymus
4	chr8:9428200-9466200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:9428400-9450000	Weak transcription	Psoas Muscle	Psoas
6	chr8:9429000-9450000	Weak transcription	Fetal Kidney	kidney
7	chr8:9430200-9442400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr8:9430200-9449800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr8:9431000-9447000	Weak transcription	Brain Substantia Nigra	brain
10	chr8:9431000-9448800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr8:9431000-9449400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr8:9431000-9450000	Weak transcription	Colon Smooth Muscle	Colon
13	chr8:9432000-9444400	Weak transcription	NHEK	skin
14	chr8:9432000-9448200	Weak transcription	Fetal Brain Male	brain
15	chr8:9433600-9461000	Weak transcription	Fetal Stomach	stomach
16	chr8:9434800-9459000	Weak transcription	Primary B cells from cord blood	blood
17	chr8:9435200-9444000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr8:9435200-9446000	Weak transcription	Fetal Thymus	thymus
19	chr8:9435200-9448800	Weak transcription	HUVEC	blood vessel
20	chr8:9435400-9448800	Weak transcription	NHLF	lung
21	chr8:9435400-9449800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr8:9435400-9465600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:9435400-9468400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr8:9435600-9448800	Weak transcription	A549	lung
25	chr8:9435600-9449000	Weak transcription	Liver	Liver
26	chr8:9435600-9449600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr8:9435600-9450000	Weak transcription	Small Intestine	intestine
28	chr8:9435600-9457600	Weak transcription	Fetal Muscle Leg	muscle
29	chr8:9435600-9472400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr8:9435800-9442200	Weak transcription	Aorta	Aorta
31	chr8:9435800-9442600	Weak transcription	Placenta	Placenta
32	chr8:9435800-9446000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr8:9435800-9447000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr8:9435800-9447400	Weak transcription	Gastric	stomach
35	chr8:9435800-9447400	Weak transcription	Ovary	ovary
36	chr8:9435800-9447400	Weak transcription	Right Atrium	heart
37	chr8:9435800-9448800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr8:9435800-9448800	Weak transcription	Spleen	Spleen
39	chr8:9435800-9449600	Weak transcription	Stomach Mucosa	stomach
40	chr8:9435800-9459400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr8:9435800-9465400	Weak transcription	Lung	lung
42	chr8:9435800-9465600	Weak transcription	Pancreas	Pancrea
43	chr8:9435800-9472600	Weak transcription	HSMMtube	muscle
44	chr8:9436000-9442800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr8:9436000-9443000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr8:9436000-9444400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr8:9436000-9446600	Weak transcription	Fetal Heart	heart
48	chr8:9436000-9446600	Weak transcription	Fetal Intestine Small	intestine
49	chr8:9436000-9449600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr8:9436400-9446000	Weak transcription	Hela-S3	cervix

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