Variant report

Variant	rs16851294
Chromosome Location	chr3:140997752-140997753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140995854..140998314-chr3:141085270..141088004,2	K562	blood:
2	chr3:140948408..140951597-chr3:140996026..140999585,4	MCF-7	breast:
3	chr3:140945385..140947466-chr3:140997029..140999166,2	MCF-7	breast:
4	chr3:140996819..140999221-chr3:141004642..141007259,2	MCF-7	breast:
5	chr3:140992520..140994223-chr3:140997053..141000025,2	K562	blood:
6	chr3:140991760..140994020-chr3:140996635..140998553,2	K562	blood:
7	chr3:140995281..140996903-chr3:140996967..140998531,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177311	Chromatin interaction
ENSG00000155893	Chromatin interaction
ENSG00000249417	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11556022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11709727	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11717615	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11921252	0.86[CEU][hapmap]
rs1567557	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16851272	0.87[CEU][hapmap]
rs16851304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2137015	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57758275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60025335	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60505234	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61370146	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6792660	0.96[AFR][1000 genomes]
rs6794495	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs72982595	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72982597	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72984505	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv877551	chr3:140970556-141029860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16851294	ACPL2	cis	cerebellum	SCAN
rs16851294	TRPC1	cis	parietal	SCAN
rs16851294	PLS1	cis	parietal	SCAN
rs16851294	ACPL2	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
4	chr3:140978000-140998000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:140979000-141000800	Weak transcription	Fetal Kidney	kidney
6	chr3:140979000-141013200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:140980800-141005600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:140981000-140998400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:140981200-141013200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:140981200-141013400	Weak transcription	Colonic Mucosa	Colon
11	chr3:140981400-141001000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:140983600-141021600	Weak transcription	Esophagus	oesophagus
13	chr3:140984200-141000800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:140984800-141006400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:140986200-140998000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:140986200-141000800	Weak transcription	Fetal Lung	lung
17	chr3:140988200-141022600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:140988400-141001800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:140990800-140998600	Weak transcription	Gastric	stomach
20	chr3:140991000-140997800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:140991000-140999600	Weak transcription	Pancreas	Pancrea
22	chr3:140993200-141014200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:140993400-140998400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:140993600-141004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:140993800-140998400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:140993800-140998600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:140993800-140999600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:140994000-141006000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:140994200-140997800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:140994200-140999400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:140994400-140997800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:140994400-140997800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:140994400-140997800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:140994400-140998000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:140994400-140998000	Weak transcription	NH-A	brain
36	chr3:140994400-140998200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:140994400-141000200	Weak transcription	Ovary	ovary
38	chr3:140994400-141005600	Weak transcription	GM12878-XiMat	blood
39	chr3:140994400-141009000	Strong transcription	Dnd41	blood
40	chr3:140994600-140997800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:140994600-140997800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:140994600-140997800	Weak transcription	HSMM	muscle
43	chr3:140994600-141006800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:140994600-141012400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:140994600-141013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:140995200-141007000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:140995400-141009000	Weak transcription	HepG2	liver
48	chr3:140995600-140998400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:140996000-141012400	Strong transcription	Thymus	Thymus
50	chr3:140996200-140998400	Enhancers	Primary neutrophils fromperipheralblood	blood

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