Variant report

Variant	rs3777585
Chromosome Location	chr6:45918969-45918970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10948265	0.83[AMR][1000 genomes]
rs1555213	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2095771	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3777567	1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes]
rs3777568	0.83[AMR][1000 genomes]
rs3777573	0.94[TSI][hapmap]
rs3798262	1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes]
rs9349337	1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][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	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3777585	PTCRA	cis	parietal	SCAN
rs3777585	CDC5L	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45898800-45919200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:45911000-45919200	Weak transcription	Small Intestine	intestine
3	chr6:45911000-45923600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:45911400-45919000	Weak transcription	Adipose Nuclei	Adipose
5	chr6:45912600-45923000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
6	chr6:45912800-45928400	Weak transcription	Spleen	Spleen
7	chr6:45913400-45919000	Strong transcription	Fetal Intestine Small	intestine
8	chr6:45913800-45920000	Enhancers	Placenta	Placenta
9	chr6:45914200-45919200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:45914600-45919400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:45915000-45919200	Weak transcription	Lung	lung
12	chr6:45915200-45919000	Weak transcription	Right Atrium	heart
13	chr6:45915400-45919000	Weak transcription	Fetal Heart	heart
14	chr6:45915800-45919800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:45916200-45919400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:45916800-45919000	Weak transcription	Right Ventricle	heart
17	chr6:45917200-45919000	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:45917200-45919000	Weak transcription	Left Ventricle	heart
19	chr6:45917200-45919000	Weak transcription	Pancreas	Pancrea
20	chr6:45917200-45919000	Weak transcription	Psoas Muscle	Psoas
21	chr6:45917200-45919200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:45917200-45919200	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr6:45917200-45924800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr6:45917400-45919000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:45917400-45919000	Weak transcription	HSMMtube	muscle
26	chr6:45917400-45919200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:45918000-45919000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:45918200-45920000	Enhancers	Colonic Mucosa	Colon
29	chr6:45918800-45919200	Enhancers	Fetal Kidney	kidney
30	chr6:45918800-45919200	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr6:45918800-45919200	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr6:45918800-45919400	Genic enhancers	Fetal Intestine Large	intestine
33	chr6:45918800-45920000	Enhancers	Stomach Smooth Muscle	stomach
34	chr6:45918800-45920200	Enhancers	Fetal Lung	lung
35	chr6:45918800-45938400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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