Variant report

Variant	rs2056659
Chromosome Location	chr7:98719597-98719598
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:98719225..98722098-chr7:98723102..98725417,4	K562	blood:
2	chr7:98718671..98728659-chr7:98733886..98742869,16	K562	blood:
3	chr7:98718971..98721801-chr7:98724719..98728203,3	MCF-7	breast:
4	chr7:98718886..98722189-chr7:98739592..98743247,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198742	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10808110	0.87[ASN][1000 genomes]
rs10953281	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs10953283	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs12705030	0.83[ASN][1000 genomes]
rs12705031	0.83[ASN][1000 genomes]
rs13222381	1.00[JPT][hapmap]
rs17147666	1.00[JPT][hapmap]
rs4729515	0.85[ASN][1000 genomes]
rs4729516	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs4729521	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[YRI][hapmap]
rs6952161	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs7794690	0.83[ASN][1000 genomes]
rs7807000	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs941001	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024529	chr7:98194830-98793518	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv539036	chr7:98194830-98793518	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2056659	BAIAP2L1	cis	parietal	SCAN
rs2056659	C7orf52	cis	cerebellum	SCAN
rs2056659	PILRB	cis	parietal	SCAN
rs2056659	MUC17	cis	cerebellum	SCAN
rs2056659	KDM5B	trans	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98707200-98739400	Weak transcription	Thymus	Thymus
2	chr7:98709800-98721000	Weak transcription	Colonic Mucosa	Colon
3	chr7:98710000-98721400	Weak transcription	Esophagus	oesophagus
4	chr7:98710000-98721400	Weak transcription	Pancreas	Pancrea
5	chr7:98710000-98739200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr7:98710200-98720400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr7:98710200-98721000	Weak transcription	HMEC	breast
8	chr7:98710200-98721600	Weak transcription	Fetal Thymus	thymus
9	chr7:98710200-98723200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:98710200-98723200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:98710200-98723400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:98710400-98721000	Weak transcription	HUVEC	blood vessel
13	chr7:98710400-98721400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr7:98710400-98721800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:98710400-98730400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:98711000-98723200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr7:98714400-98730600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:98714800-98739400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:98715200-98721800	Weak transcription	Fetal Intestine Large	intestine
20	chr7:98715400-98719800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr7:98715600-98719800	Enhancers	Adipose Nuclei	Adipose
22	chr7:98717000-98719600	Enhancers	Brain Anterior Caudate	brain
23	chr7:98717000-98720000	Enhancers	Stomach Mucosa	stomach
24	chr7:98717000-98731000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:98717200-98719600	Enhancers	Brain Substantia Nigra	brain
26	chr7:98717200-98719800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:98717400-98719600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr7:98717400-98724200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:98717600-98719600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:98717600-98719600	Enhancers	Brain Angular Gyrus	brain
31	chr7:98717600-98719600	Enhancers	Brain Cingulate Gyrus	brain
32	chr7:98717600-98719600	Enhancers	Rectal Smooth Muscle	rectum
33	chr7:98717800-98719600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:98717800-98719600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr7:98717800-98721200	Weak transcription	Hela-S3	cervix
36	chr7:98717800-98721600	Weak transcription	Fetal Intestine Small	intestine
37	chr7:98718000-98719600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr7:98718000-98719600	Enhancers	HSMM	muscle
39	chr7:98718000-98719600	Enhancers	NH-A	brain
40	chr7:98718000-98719800	Enhancers	Brain Hippocampus Middle	brain
41	chr7:98718000-98719800	Enhancers	Fetal Stomach	stomach
42	chr7:98718000-98722800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr7:98718000-98723200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:98718200-98719600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:98718200-98719600	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr7:98718200-98719600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr7:98718200-98719600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:98718200-98719600	Enhancers	Fetal Heart	heart
49	chr7:98718200-98720400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:98718200-98723000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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