Variant report

Variant	rs11974610
Chromosome Location	chr7:99527977-99527978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99525940-99530576	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:99523651..99525447-chr7:99527733..99529553,2	MCF-7	breast:
2	chr7:99527800..99529486-chr7:99535396..99536923,2	MCF-7	breast:
3	chr7:99102673..99104536-chr7:99527023..99529277,2	K562	blood:
4	chr7:99516373..99518642-chr7:99525768..99528008,3	MCF-7	breast:

Variant related genes	Relation type
GJC3	TF binding region
ENSG00000146833	Chromatin interaction
ENSG00000196652	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10243988	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275719	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10953292	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13230989	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2082743	0.89[YRI][hapmap]
rs35286301	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4336540	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57075121	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6957718	0.89[YRI][hapmap]
rs7787525	0.88[LWK][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv607930	chr7:99525241-99602191	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11974610	FAM200A	cis	cerebellum	SCAN
rs11974610	OR2AE1	cis	cerebellum	SCAN
rs11974610	GATS	cis	cerebellum	SCAN
rs11974610	OR2AE1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99526400-99528000	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr7:99526600-99528600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr7:99526800-99528000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:99526800-99528000	Enhancers	Brain Angular Gyrus	brain
5	chr7:99526800-99528000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
6	chr7:99527000-99528000	Enhancers	Brain Cingulate Gyrus	brain
7	chr7:99527200-99528000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:99527200-99528000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:99527200-99528000	Enhancers	Fetal Kidney	kidney
10	chr7:99527400-99528000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr7:99527400-99528000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr7:99527400-99528000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:99527400-99528000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr7:99527400-99528000	Enhancers	Brain Anterior Caudate	brain
15	chr7:99527400-99528000	Enhancers	Brain Hippocampus Middle	brain
16	chr7:99527400-99528000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr7:99527400-99528000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr7:99527400-99528000	Enhancers	Fetal Heart	heart
19	chr7:99527400-99528000	Enhancers	Fetal Intestine Small	intestine
20	chr7:99527400-99528000	Enhancers	Fetal Stomach	stomach
21	chr7:99527400-99528200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr7:99527600-99528000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr7:99527600-99528000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr7:99527600-99528000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:99527600-99528000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:99527600-99528200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:99527600-99528200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr7:99527600-99528400	Enhancers	Primary T cells from cord blood	blood
29	chr7:99527600-99528400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr7:99527600-99528400	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr7:99527600-99529000	Weak transcription	K562	blood
32	chr7:99527600-99532200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:99527600-99532400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:99527800-99528000	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr7:99527800-99528000	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr7:99527800-99528000	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr7:99527800-99528000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:99527800-99528000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr7:99527800-99528000	Enhancers	Colon Smooth Muscle	Colon
40	chr7:99527800-99528000	Enhancers	Rectal Smooth Muscle	rectum
41	chr7:99527800-99528200	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr7:99527800-99528200	Enhancers	HepG2	liver
43	chr7:99527800-99528600	Enhancers	HSMMtube	muscle
44	chr7:99527800-99531600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr7:99527800-99532200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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