Variant report

Variant	rs227851
Chromosome Location	chr6:44699209-44699210
allele	A/C
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: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1022730	0.95[ASN][1000 genomes]
rs1022731	0.95[ASN][1000 genomes]
rs12215252	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1338907	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1342640	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1418433	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1832897	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2145826	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs227831	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227837	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs227838	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227841	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs227843	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs227847	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227848	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227849	0.92[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs227850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227854	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs227855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799968	0.81[CEU][hapmap]
rs6458412	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6910294	0.84[CEU][hapmap]
rs911524	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9349303	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9369514	0.81[CEU][hapmap]
rs9369515	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs9463011	0.80[ASN][1000 genomes]
rs9472339	0.92[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs227851	SUPT3H	cis	multi-tissue	Pritchard
rs227851	SUPT3H	cis	cerebellum	SCAN
rs227851	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs227851	SUPT3H	cis	parietal	SCAN
rs227851	C6orf226	cis	cerebellum	SCAN
rs227851	SUPT3H	cis	lymphoblastoid	seeQTL

Chromatin state (count:35 , 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	chr6:44698200-44699600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:44698200-44699600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr6:44698200-44699600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:44698200-44699800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:44698200-44699800	Enhancers	HSMM	muscle
13	chr6:44698200-44703800	Enhancers	Placenta	Placenta
14	chr6:44698400-44699400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:44698400-44699600	Enhancers	Fetal Intestine Small	intestine
16	chr6:44698400-44699600	Enhancers	Fetal Stomach	stomach
17	chr6:44698400-44699800	Enhancers	Fetal Intestine Large	intestine
18	chr6:44698400-44699800	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr6:44698400-44699800	Enhancers	Rectal Smooth Muscle	rectum
20	chr6:44698400-44699800	Enhancers	NHLF	lung
21	chr6:44698400-44699800	Enhancers	Osteobl	bone
22	chr6:44698400-44700200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr6:44698400-44700600	Enhancers	Fetal Muscle Trunk	muscle
24	chr6:44698600-44699600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:44698600-44701200	Weak transcription	Fetal Lung	lung
26	chr6:44698600-44701200	Weak transcription	GM12878-XiMat	blood
27	chr6:44698800-44699400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:44698800-44699400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr6:44698800-44699600	Enhancers	Psoas Muscle	Psoas
30	chr6:44699000-44699600	Enhancers	Colonic Mucosa	Colon
31	chr6:44699000-44700000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr6:44699200-44699800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:44699200-44700200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:44699200-44701600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:44699200-44703200	Enhancers	Fetal Muscle Leg	muscle

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