Variant report

Variant	rs543134
Chromosome Location	chr2:30917735-30917736
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30911934..30915196-chr2:30916414..30919357,3	K562	blood:
2	chr2:30884077..30886953-chr2:30917137..30920248,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LCLAT1-1	chr2:30916445-30920389	XLOC_001413

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1252298	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs485243	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs497707	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs514940	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs528264	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs528514	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs537833	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs540977	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs544395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs546467	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs547360	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs566241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs566934	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs578011	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs935984	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs543134	KHK	cis	cerebellum	SCAN
rs543134	CCDC121	cis	cerebellum	SCAN
rs543134	RBKS	cis	parietal	SCAN
rs543134	LCLAT1	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30902400-30954000	Weak transcription	Gastric	stomach
2	chr2:30910600-30918200	Enhancers	Right Ventricle	heart
3	chr2:30913400-30917800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:30915000-30918200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:30915200-30918400	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr2:30915600-30918400	Enhancers	NHDF-Ad	bronchial
7	chr2:30916600-30918200	Enhancers	Right Atrium	heart
8	chr2:30916600-30918200	Enhancers	Stomach Smooth Muscle	stomach
9	chr2:30916600-30918400	Enhancers	Left Ventricle	heart
10	chr2:30916800-30918000	Enhancers	Osteobl	bone
11	chr2:30916800-30918200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:30916800-30918400	Enhancers	Aorta	Aorta
13	chr2:30916800-30918600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr2:30917000-30918000	Enhancers	HSMM	muscle
15	chr2:30917000-30918200	Enhancers	Fetal Muscle Leg	muscle
16	chr2:30917000-30918200	Enhancers	HSMMtube	muscle
17	chr2:30917000-30918400	Enhancers	Psoas Muscle	Psoas
18	chr2:30917200-30917800	Enhancers	Fetal Lung	lung
19	chr2:30917200-30918000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:30917200-30918000	Enhancers	Colon Smooth Muscle	Colon
21	chr2:30917200-30918200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:30917200-30918200	Enhancers	Fetal Brain Male	brain
23	chr2:30917200-30918200	Enhancers	Rectal Smooth Muscle	rectum
24	chr2:30917200-30918400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:30917200-30918600	Enhancers	Fetal Heart	heart
26	chr2:30917400-30917800	Enhancers	NH-A	brain
27	chr2:30917400-30920200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:30917600-30918000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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