Variant report

Variant	rs227850
Chromosome Location	chr6:44699068-44699069
allele	A/G
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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDC5L-2	chr6:44698855-44699105	XLOC_005299

Variant related genes	Relation type
ENSG00000271857	Chromatin interaction
ENSG00000124813	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1022730	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1022731	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12215252	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1338907	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1342640	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1418433	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1832897	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2145826	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs227831	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs227837	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs227838	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs227841	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs227843	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227849	0.93[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs227851	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	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs227855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778507	0.80[TSI][hapmap]
rs3799968	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs57020561	0.81[AMR][1000 genomes]
rs6458412	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6910294	0.85[CEU][hapmap]
rs911524	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349303	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9369514	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs9369515	0.91[CHB][hapmap];0.84[AMR][1000 genomes]
rs9369516	0.80[TSI][hapmap]
rs9395051	0.80[TSI][hapmap]
rs9463011	0.81[AMR][1000 genomes]
rs9472339	0.92[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs227850	C6orf226	cis	cerebellum	SCAN
rs227850	SUPT3H	cis	cerebellum	SCAN
rs227850	SUPT3H	cis	lymphoblastoid	seeQTL
rs227850	SUPT3H	cis	parietal	SCAN

Chromatin state (count:39 , 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	chr6:44698200-44699200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:44698200-44699200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:44698200-44699200	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr6:44698200-44699200	Enhancers	NH-A	brain
12	chr6:44698200-44699600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:44698200-44699600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:44698200-44699600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:44698200-44699800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:44698200-44699800	Enhancers	HSMM	muscle
17	chr6:44698200-44703800	Enhancers	Placenta	Placenta
18	chr6:44698400-44699200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:44698400-44699400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:44698400-44699600	Enhancers	Fetal Intestine Small	intestine
21	chr6:44698400-44699600	Enhancers	Fetal Stomach	stomach
22	chr6:44698400-44699800	Enhancers	Fetal Intestine Large	intestine
23	chr6:44698400-44699800	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr6:44698400-44699800	Enhancers	Rectal Smooth Muscle	rectum
25	chr6:44698400-44699800	Enhancers	NHLF	lung
26	chr6:44698400-44699800	Enhancers	Osteobl	bone
27	chr6:44698400-44700200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr6:44698400-44700600	Enhancers	Fetal Muscle Trunk	muscle
29	chr6:44698600-44699600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:44698600-44701200	Weak transcription	Fetal Lung	lung
31	chr6:44698600-44701200	Weak transcription	GM12878-XiMat	blood
32	chr6:44698800-44699200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:44698800-44699400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:44698800-44699400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr6:44698800-44699600	Enhancers	Psoas Muscle	Psoas
36	chr6:44699000-44699200	Enhancers	Duodenum Mucosa	Duodenum
37	chr6:44699000-44699200	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr6:44699000-44699600	Enhancers	Colonic Mucosa	Colon
39	chr6:44699000-44700000	Enhancers	Skeletal Muscle Female	skeletal muscle

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