Variant report

Variant	rs1148
Chromosome Location	chr6:163789521-163789522
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1737319	0.89[TSI][hapmap]
rs1737324	0.89[TSI][hapmap]
rs1764010	0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1022610	chr6:163591786-163814041	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1148	GCHFR	trans	parietal	SCAN
rs1148	QKI	Cis_1M	lymphoblastoid	RTeQTL
rs1148	UNC93A	cis	parietal	SCAN
rs1148	SYNPR	trans	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163777400-163790000	Weak transcription	Spleen	Spleen
2	chr6:163777400-163791400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:163778400-163790800	Weak transcription	Right Atrium	heart
4	chr6:163783800-163791800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:163784000-163789600	Weak transcription	Brain Anterior Caudate	brain
6	chr6:163784000-163791000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:163784200-163790000	Weak transcription	Brain Angular Gyrus	brain
8	chr6:163787600-163791800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:163788000-163791000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:163788200-163789600	Weak transcription	Brain Substantia Nigra	brain
11	chr6:163788400-163790000	Enhancers	HUVEC	blood vessel
12	chr6:163788800-163789600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:163789000-163789800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:163789000-163790800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:163789000-163790800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:163789000-163791600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:163789200-163789600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:163789200-163789600	Weak transcription	Brain Hippocampus Middle	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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