Variant report

Variant	rs227853
Chromosome Location	chr6:44699746-44699747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44629072..44631596-chr6:44697653..44700254,3	MCF-7	breast:
2	chr6:44698581..44700175-chr6:45387689..45389869,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124813	Chromatin interaction
ENSG00000271857	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12192367	0.83[JPT][hapmap]
rs12529522	0.88[CHB][hapmap]
rs12530016	0.88[CHB][hapmap]
rs13206206	0.94[ASN][1000 genomes]
rs13206526	0.94[CHB][hapmap];0.86[MEX][hapmap]
rs1402599	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap]
rs1418435	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16869119	1.00[CHB][hapmap]
rs1935549	0.82[AMR][1000 genomes]
rs2139863	1.00[CHB][hapmap]
rs227830	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs227832	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227833	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227835	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227836	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227839	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227840	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227844	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs227845	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227849	0.90[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs227852	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227854	0.84[CEU][hapmap];0.92[EUR][1000 genomes]
rs227857	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34577161	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35376827	0.94[ASN][1000 genomes]
rs3799965	1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap]
rs3799968	0.89[CHD][hapmap]
rs3799972	1.00[CHB][hapmap]
rs3799974	1.00[CHB][hapmap]
rs3823252	1.00[CHB][hapmap];0.86[MEX][hapmap]
rs3997503	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711797	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4714812	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4714813	0.92[EUR][1000 genomes]
rs4714825	0.82[AMR][1000 genomes]
rs524492	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap]
rs542444	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap]
rs609643	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs609699	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs687878	0.91[EUR][1000 genomes]
rs6919161	0.94[CHB][hapmap]
rs72664272	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7746032	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7769218	1.00[CHB][hapmap]
rs9369514	0.87[CHD][hapmap]
rs9463017	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9463039	0.84[AMR][1000 genomes]
rs9463040	0.84[AMR][1000 genomes]
rs9472331	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9472335	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9472376	0.94[CHB][hapmap];0.82[CHD][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs227853	SPATS1	cis	cerebellum	SCAN
rs227853	SUPT3H	cis	multi-tissue	Pritchard
rs227853	SUPT3H	cis	lymphoblastoid	seeQTL
rs227853	SLC22A7	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44695800-44701000	Weak transcription	Pancreas	Pancrea
2	chr6:44695800-44703600	Weak transcription	Esophagus	oesophagus
3	chr6:44696000-44706000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:44697600-44699800	Enhancers	Fetal Kidney	kidney
5	chr6:44697800-44704200	Enhancers	Colon Smooth Muscle	Colon
6	chr6:44698000-44700000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr6:44698000-44700400	Enhancers	HSMMtube	muscle
8	chr6:44698200-44699800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:44698200-44699800	Enhancers	HSMM	muscle
10	chr6:44698200-44703800	Enhancers	Placenta	Placenta
11	chr6:44698400-44699800	Enhancers	Fetal Intestine Large	intestine
12	chr6:44698400-44699800	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr6:44698400-44699800	Enhancers	Rectal Smooth Muscle	rectum
14	chr6:44698400-44699800	Enhancers	NHLF	lung
15	chr6:44698400-44699800	Enhancers	Osteobl	bone
16	chr6:44698400-44700200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr6:44698400-44700600	Enhancers	Fetal Muscle Trunk	muscle
18	chr6:44698600-44701200	Weak transcription	Fetal Lung	lung
19	chr6:44698600-44701200	Weak transcription	GM12878-XiMat	blood
20	chr6:44699000-44700000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr6:44699200-44699800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:44699200-44700200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:44699200-44701600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:44699200-44703200	Enhancers	Fetal Muscle Leg	muscle
25	chr6:44699400-44701400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:44699400-44701800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:44699600-44699800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:44699600-44701000	Weak transcription	Fetal Stomach	stomach
29	chr6:44699600-44701400	Weak transcription	Colonic Mucosa	Colon

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