Variant report

Variant	rs634904
Chromosome Location	chr1:84722102-84722103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1027694	0.89[CEU][hapmap]
rs1085727	0.88[ASN][1000 genomes]
rs11163930	0.97[ASN][1000 genomes]
rs12411158	0.88[ASN][1000 genomes]
rs1402695	0.99[ASN][1000 genomes]
rs1402697	0.90[ASN][1000 genomes]
rs2389717	0.89[CEU][hapmap]
rs316630	0.92[ASN][1000 genomes]
rs4907050	0.92[ASN][1000 genomes]
rs600674	0.89[CEU][hapmap]
rs657321	0.92[ASN][1000 genomes]
rs677124	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7526798	0.80[ASN][1000 genomes]
rs7549996	0.81[ASN][1000 genomes]
rs787858	0.95[CHB][hapmap];0.89[GIH][hapmap];0.88[ASN][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	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs634904	CLCA1	cis	cerebellum	SCAN
rs634904	DNASE2B	cis	cerebellum	SCAN
rs634904	PRKACB	cis	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84705800-84723000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:84714000-84726000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:84718200-84723400	Enhancers	Brain Substantia Nigra	brain
4	chr1:84720000-84722200	Weak transcription	Gastric	stomach
5	chr1:84720000-84725600	Weak transcription	Pancreas	Pancrea
6	chr1:84720200-84723400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:84720600-84727400	Weak transcription	Aorta	Aorta
8	chr1:84721000-84723200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:84721200-84723200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:84721400-84723000	Weak transcription	Brain Anterior Caudate	brain
11	chr1:84721400-84723000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:84721400-84725400	Weak transcription	A549	lung
13	chr1:84721600-84722600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:84721600-84722600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:84721600-84723000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:84721600-84726000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:84721600-84728200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:84721800-84722400	Weak transcription	Stomach Mucosa	stomach
19	chr1:84722000-84722400	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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