Variant report

Variant	rs6750698
Chromosome Location	chr2:46779051-46779052
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46776310..46779098-chr2:46785814..46787869,2	MCF-7	breast:
2	chr2:46778318..46780393-chr2:46788541..46791155,3	K562	blood:
3	chr2:46769168..46772138-chr2:46777700..46782112,5	MCF-7	breast:
4	chr2:46778318..46780093-chr2:46788541..46791155,2	K562	blood:

Variant related genes	Relation type
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12105801	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12712976	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13420857	0.80[EUR][1000 genomes]
rs1451153	0.91[EUR][1000 genomes]
rs4384837	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6725948	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6734476	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	nsv9713	chr2:46775356-46790566	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6750698	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs6750698	PIGF	Cis_1M	lymphoblastoid	RTeQTL
rs6750698	CRIPT	cis	Stomach	GTEx
rs6750698	CRIPT	cis	multi-tissue	Pritchard
rs6750698	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs6750698	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs6750698	PIGF	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46771000-46781600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:46771200-46780000	Enhancers	Psoas Muscle	Psoas
3	chr2:46771200-46781400	Weak transcription	NHEK	skin
4	chr2:46771200-46781600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:46771200-46781600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:46771400-46780000	Genic enhancers	Fetal Muscle Leg	muscle
8	chr2:46771400-46781600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:46771400-46789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:46771400-46796000	Weak transcription	Fetal Kidney	kidney
11	chr2:46771600-46781600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:46771600-46781600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:46771800-46780000	Enhancers	Right Atrium	heart
14	chr2:46771800-46781400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:46771800-46781400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:46771800-46781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:46771800-46782000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:46771800-46782400	Weak transcription	HMEC	breast
19	chr2:46771800-46795600	Weak transcription	Fetal Brain Male	brain
20	chr2:46772000-46782600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:46772200-46780200	Genic enhancers	Left Ventricle	heart
22	chr2:46772200-46804000	Weak transcription	NH-A	brain
23	chr2:46773000-46780200	Strong transcription	Osteobl	bone
24	chr2:46773200-46806000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:46773400-46779800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:46774000-46779800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:46774400-46782200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:46774600-46780000	Genic enhancers	Spleen	Spleen
29	chr2:46774800-46781400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:46774800-46789200	Weak transcription	Pancreas	Pancrea
31	chr2:46775200-46782400	Weak transcription	Fetal Lung	lung
32	chr2:46775200-46787200	Weak transcription	Gastric	stomach
33	chr2:46775200-46788600	Weak transcription	A549	lung
34	chr2:46775400-46779400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:46775400-46782600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
37	chr2:46775800-46779600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:46775800-46780200	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr2:46776000-46781400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:46776400-46779400	Weak transcription	Fetal Intestine Small	intestine
41	chr2:46776400-46779800	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr2:46776400-46780000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:46776400-46780000	Genic enhancers	Monocytes-CD14+_RO01746	blood
44	chr2:46776400-46780200	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr2:46776400-46784800	Weak transcription	Dnd41	blood
46	chr2:46776400-46789000	Weak transcription	Primary T cells from cord blood	blood
47	chr2:46776600-46780200	Strong transcription	NHLF	lung
48	chr2:46776600-46782400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:46776600-46784800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:46776600-46785000	Weak transcription	Liver	Liver

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