Variant report

Variant	rs13220304
Chromosome Location	chr6:109652236-109652237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10782162	0.80[CEU][hapmap];0.81[MKK][hapmap]
rs11753645	0.89[CEU][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs11757877	0.84[CEU][hapmap]
rs12524502	0.95[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12528712	0.89[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13195517	0.89[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap]
rs13199519	0.89[CEU][hapmap]
rs13203252	0.88[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs17534632	0.81[MEX][hapmap]
rs34131679	0.80[EUR][1000 genomes]
rs3799835	0.89[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs61233650	0.80[EUR][1000 genomes]
rs67857472	0.80[EUR][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	nsv5435	chr6:109633035-109669127	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs13220304	PPIL6	cis	cerebellum	SCAN
rs13220304	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs13220304	AKD1	cis	cerebellum	SCAN
rs13220304	SMPD2	cis	multi-tissue	Pritchard
rs13220304	SMPD2	cis	cerebellum	SCAN
rs13220304	CD164	cis	parietal	SCAN
rs13220304	MICAL1	cis	parietal	SCAN
rs13220304	SMPD2	cis	parietal	SCAN
rs13220304	PDSS2	cis	cerebellum	SCAN
rs13220304	SMPD2	cis	Whole Blood	GTEx
rs13220304	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs13220304	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109629600-109654000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:109641000-109653600	Weak transcription	Small Intestine	intestine
3	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
4	chr6:109644800-109657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:109645400-109653600	Weak transcription	Spleen	Spleen
6	chr6:109645400-109662400	Weak transcription	Aorta	Aorta
7	chr6:109649200-109654000	Weak transcription	K562	blood
8	chr6:109649600-109653800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:109650200-109653000	Weak transcription	Fetal Intestine Large	intestine
10	chr6:109650200-109653600	Weak transcription	HepG2	liver
11	chr6:109650200-109653800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:109650600-109653000	Weak transcription	Fetal Intestine Small	intestine
13	chr6:109651600-109653600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:109651600-109654600	Enhancers	Stomach Mucosa	stomach
15	chr6:109651800-109653600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:109651800-109653800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:109652000-109653600	Weak transcription	Primary monocytes fromperipheralblood	blood

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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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