Variant report

Variant	rs10495934
Chromosome Location	chr2:46874746-46874747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46872495..46874222-chr2:46874302..46877114,2	MCF-7	breast:
2	chr2:46863139..46865954-chr2:46873565..46877527,3	K562	blood:
3	chr2:46861539..46864465-chr2:46873004..46877415,5	MCF-7	breast:
4	chr2:46867092..46870472-chr2:46872248..46874879,4	MCF-7	breast:
5	chr2:46867409..46869384-chr2:46873725..46875843,2	MCF-7	breast:
6	chr2:46870874..46873368-chr2:46874552..46876538,2	K562	blood:
7	chr2:46874572..46876789-chr2:46877093..46878629,2	MCF-7	breast:
8	chr2:46842547..46845203-chr2:46873020..46875876,4	MCF-7	breast:
9	chr2:46870874..46873368-chr2:46874552..46876538,3	K562	blood:
10	chr2:46873644..46875189-chr2:46880714..46882765,2	MCF-7	breast:
11	chr2:46872845..46875146-chr2:46877009..46879600,2	K562	blood:
12	chr2:46864993..46867053-chr2:46871830..46874793,2	K562	blood:
13	chr2:46872423..46876181-chr2:46924368..46927720,4	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRIPT-1	chr2:46874377-46875527	NONHSAT070518

No data

Variant related genes	Relation type
ENSG00000119878	Chromatin interaction
ENSG00000151665	Chromatin interaction
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12105006	0.82[ASN][1000 genomes]
rs13417558	0.85[EUR][1000 genomes]
rs17768226	0.90[EUR][1000 genomes]
rs17818399	0.90[CHB][hapmap]
rs1869836	0.94[ASN][1000 genomes]
rs2346419	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2881504	0.96[ASN][1000 genomes]
rs55742873	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60786889	0.86[ASN][1000 genomes]
rs6544909	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6544910	0.96[ASN][1000 genomes]
rs6712910	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7560464	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs982395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
rs10495934	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs10495934	CRIPT	cis	multi-tissue	Pritchard
rs10495934	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs10495934	CRIPT	cis	parietal	SCAN
rs10495934	CRIPT	cis	cerebellum	SCAN
rs10495934	CRIPT	cis	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46849000-46877200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:46854800-46878600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr2:46858000-46874800	Weak transcription	Liver	Liver
4	chr2:46862400-46877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:46869400-46883400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:46869600-46876800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:46869600-46881200	Weak transcription	Primary T cells from cord blood	blood
8	chr2:46869800-46878400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:46869800-46882200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:46870000-46877200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:46870000-46880800	Weak transcription	Primary B cells from cord blood	blood
12	chr2:46870000-46891000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:46870200-46889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:46870400-46878200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:46870800-46876000	Enhancers	Osteobl	bone
16	chr2:46870800-46876400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:46871000-46877400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:46871400-46876000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:46871600-46875000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:46871600-46876200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:46871800-46875400	Enhancers	HMEC	breast
22	chr2:46871800-46876000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:46872000-46875800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:46872000-46883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:46872800-46876000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:46872800-46877600	Enhancers	Fetal Brain Male	brain
27	chr2:46873000-46875600	Enhancers	NHEK	skin
28	chr2:46873000-46880600	Weak transcription	Right Atrium	heart
29	chr2:46873200-46879000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:46873200-46879800	Weak transcription	Psoas Muscle	Psoas
31	chr2:46873400-46875200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:46873400-46878000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:46873400-46878200	Weak transcription	Adipose Nuclei	Adipose
34	chr2:46873400-46878200	Weak transcription	Ovary	ovary
35	chr2:46873400-46878400	Weak transcription	Fetal Stomach	stomach
36	chr2:46873400-46878600	Weak transcription	HSMM	muscle
37	chr2:46873400-46878800	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:46873400-46881800	Weak transcription	Brain Angular Gyrus	brain
39	chr2:46873400-46883400	Weak transcription	Right Ventricle	heart
40	chr2:46873400-46884000	Weak transcription	Brain Anterior Caudate	brain
41	chr2:46873600-46877600	Weak transcription	Fetal Lung	lung
42	chr2:46873800-46876400	Enhancers	HepG2	liver
43	chr2:46873800-46877000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:46873800-46878200	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:46874000-46880400	Weak transcription	HSMMtube	muscle
46	chr2:46874400-46874800	Enhancers	A549	lung
47	chr2:46874400-46876200	Enhancers	Fetal Brain Female	brain
48	chr2:46874400-46877600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:46874400-46878000	Weak transcription	NHDF-Ad	bronchial
50	chr2:46874400-46878400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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