Variant report

Variant	rs17768138
Chromosome Location	chr2:46868217-46868218
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	chr2:46867409..46869384-chr2:46873725..46875843,2	MCF-7	breast:
2	chr2:46867092..46870472-chr2:46872248..46874879,4	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10495935	0.81[JPT][hapmap]
rs12105006	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13013245	0.91[JPT][hapmap]
rs13024534	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13032670	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13033177	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13406427	0.84[ASN][1000 genomes]
rs13417558	0.84[ASN][1000 genomes]
rs1378764	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17035488	0.81[JPT][hapmap]
rs17767994	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17768018	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17768132	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17768226	0.86[ASN][1000 genomes]
rs17818315	0.82[CEU][hapmap]
rs17819022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1824050	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2122715	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34449783	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34748737	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34752561	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34996358	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35350086	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35449212	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35682608	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35837037	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35909669	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35949012	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4952837	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55742873	0.86[ASN][1000 genomes]
rs62136873	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62136894	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136895	0.82[ASN][1000 genomes]
rs62136898	0.84[ASN][1000 genomes]
rs6746598	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7565274	0.91[ASN][1000 genomes]
rs7605089	0.84[ASN][1000 genomes]
rs896212	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17768138	CRIPT	cis	Temporal Cortex	GTEx
rs17768138	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs17768138	CRIPT	cis	multi-tissue	Pritchard
rs17768138	CRIPT	cis	Frontal Cortex	GTEx
rs17768138	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs17768138	CRIPT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46844800-46868400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:46844800-46868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:46844800-46868800	Weak transcription	Esophagus	oesophagus
4	chr2:46844800-46872200	Weak transcription	Pancreas	Pancrea
5	chr2:46845400-46871000	Weak transcription	Stomach Mucosa	stomach
6	chr2:46845400-46873000	Weak transcription	Right Ventricle	heart
7	chr2:46845600-46868800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:46846000-46868600	Weak transcription	Fetal Intestine Small	intestine
9	chr2:46848600-46871200	Weak transcription	HSMMtube	muscle
10	chr2:46848600-46872600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:46848600-46872800	Weak transcription	Left Ventricle	heart
12	chr2:46848600-46872800	Weak transcription	Ovary	ovary
13	chr2:46848800-46871000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:46848800-46872600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:46848800-46873000	Weak transcription	Brain Angular Gyrus	brain
16	chr2:46849000-46868600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:46849000-46868600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:46849000-46877200	Weak transcription	Brain Substantia Nigra	brain
19	chr2:46849200-46869400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:46849200-46869800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:46849200-46870800	Weak transcription	Hela-S3	cervix
22	chr2:46849200-46872600	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:46849400-46872800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:46850200-46868400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:46852000-46872800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:46852400-46869400	Weak transcription	Dnd41	blood
27	chr2:46853400-46869600	Weak transcription	Brain Germinal Matrix	brain
28	chr2:46853400-46872600	Weak transcription	Brain Anterior Caudate	brain
29	chr2:46853400-46872800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:46853600-46868600	Weak transcription	Fetal Intestine Large	intestine
31	chr2:46853600-46869400	Weak transcription	NH-A	brain
32	chr2:46853800-46868600	Weak transcription	Primary B cells from cord blood	blood
33	chr2:46853800-46868800	Weak transcription	Placenta	Placenta
34	chr2:46853800-46873000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:46854400-46871800	Weak transcription	Fetal Lung	lung
36	chr2:46854600-46869000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:46854600-46869200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:46854800-46872800	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:46854800-46878600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:46855000-46868600	Weak transcription	Thymus	Thymus
41	chr2:46855200-46868400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:46856000-46868800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:46857200-46871800	Weak transcription	Adipose Nuclei	Adipose
44	chr2:46858000-46874800	Weak transcription	Liver	Liver
45	chr2:46858400-46868600	Weak transcription	Fetal Thymus	thymus
46	chr2:46858400-46868600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr2:46858400-46869400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:46858600-46868600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:46858600-46869200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr2:46858800-46868400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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