Variant report

Variant	rs353896
Chromosome Location	chr12:118634385-118634386
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:118632071..118634758-chr12:118814095..118816162,2	MCF-7	breast:
2	chr12:118626372..118631667-chr12:118631943..118636287,5	K562	blood:

Variant related genes	Relation type
ENSG00000111707	Chromatin interaction
ENSG00000135090	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1092854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1151901	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1277175	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1726386	0.83[ASN][1000 genomes]
rs1726407	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs2018619	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2088702	0.88[ASW][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs2249624	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2463173	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs353885	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs353886	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs353887	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs353889	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs353890	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs353892	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs364823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs404566	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs410747	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs418941	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs456228	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs461499	0.82[ASW][hapmap];0.86[JPT][hapmap]
rs465735	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs484838	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap]
rs492939	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap]
rs494005	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs503548	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap]
rs523011	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs566437	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs571113	0.82[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap]
rs575121	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6490167	0.83[CHB][hapmap]
rs708862	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs708863	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs795473	0.91[ASN][1000 genomes]
rs795481	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs795482	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7978165	0.83[CHB][hapmap]
rs7980628	0.85[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1054703	chr12:118575000-118638613	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv541611	chr12:118575000-118638613	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1035497	chr12:118599539-118732144	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv541612	chr12:118599539-118732144	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv524938	chr12:118624736-118740675	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs353896	GCN1L1	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118617200-118634400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:118619200-118638600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:118619400-118635200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:118619400-118635800	Weak transcription	Gastric	stomach
5	chr12:118619400-118635800	Weak transcription	Spleen	Spleen
6	chr12:118619600-118635800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:118620200-118635200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:118620200-118636800	Weak transcription	Hela-S3	cervix
9	chr12:118620200-118656400	Weak transcription	HepG2	liver
10	chr12:118621000-118682600	Weak transcription	A549	lung
11	chr12:118621400-118635800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:118622400-118643800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr12:118622400-118643800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:118622400-118646400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:118622600-118642000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:118623600-118642600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:118624400-118635400	Weak transcription	Small Intestine	intestine
18	chr12:118625600-118641600	Weak transcription	Stomach Mucosa	stomach
19	chr12:118627000-118636400	Weak transcription	K562	blood
20	chr12:118628000-118634600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:118628000-118635200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:118628000-118636600	Weak transcription	Colonic Mucosa	Colon
23	chr12:118628000-118636800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:118628000-118636800	Weak transcription	Esophagus	oesophagus
25	chr12:118628400-118635400	Weak transcription	Fetal Intestine Small	intestine
26	chr12:118628400-118636600	Weak transcription	Pancreas	Pancrea
27	chr12:118628400-118637400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:118628400-118638200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:118628400-118697200	Weak transcription	Psoas Muscle	Psoas
30	chr12:118628600-118635400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:118628600-118635600	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:118628600-118635800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:118628600-118635800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:118628600-118635800	Weak transcription	HUVEC	blood vessel
35	chr12:118628600-118636400	Weak transcription	Right Ventricle	heart
36	chr12:118628600-118636800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:118628600-118638400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:118628600-118638400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:118628600-118638400	Weak transcription	HSMMtube	muscle
40	chr12:118628600-118640200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr12:118628800-118634400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:118628800-118635200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:118628800-118635200	Weak transcription	Brain Hippocampus Middle	brain
44	chr12:118628800-118635200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:118628800-118635800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:118628800-118635800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:118628800-118635800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:118628800-118635800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:118628800-118635800	Weak transcription	Brain Substantia Nigra	brain
50	chr12:118628800-118635800	Weak transcription	Fetal Stomach	stomach

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