Variant report

Variant	rs7587836
Chromosome Location	chr2:11922855-11922856
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	CTCF	chr2:11922840-11922990	HCPEpiC	choroid plexus:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11921904..11924670-chr2:11926254..11929186,2	MCF-7	breast:

Variant related genes	Relation type
LPIN1	TF binding region
ENSG00000134324	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10520097	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs11679358	0.81[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs11690125	0.83[MEX][hapmap]
rs11694797	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695081	0.81[CEU][hapmap]
rs11695610	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs17603197	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289193	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2358125	0.96[ASN][1000 genomes]
rs3762583	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4129758	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113359	1.00[ASN][1000 genomes]
rs62114960	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7587836	FAM84A	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11906400-11924600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:11906600-11924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:11906800-11924600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:11915000-11923200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:11916800-11961200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:11918600-11923200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:11919400-11924600	Strong transcription	Fetal Stomach	stomach
8	chr2:11919400-11924800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:11919400-11925000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:11919400-11927000	Weak transcription	Fetal Heart	heart
11	chr2:11919400-11940400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:11919400-11943400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:11919400-11961800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:11919600-11923800	Strong transcription	Primary hematopoietic stem cells	blood
15	chr2:11919600-11924600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:11919600-11924600	Strong transcription	NHLF	lung
17	chr2:11919600-11924800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:11919600-11925000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:11919600-11925000	Strong transcription	Primary B cells from cord blood	blood
20	chr2:11919600-11930400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:11919600-11940800	Strong transcription	Left Ventricle	heart
22	chr2:11919600-11940800	Strong transcription	NHEK	skin
23	chr2:11919600-11968400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:11919800-11923000	Weak transcription	Pancreas	Pancrea
25	chr2:11919800-11923600	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:11919800-11923800	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr2:11919800-11924400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:11919800-11924600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:11919800-11924600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:11919800-11924600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:11919800-11924600	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:11919800-11924600	Strong transcription	HUVEC	blood vessel
33	chr2:11919800-11924800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:11919800-11924800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr2:11919800-11924800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr2:11919800-11924800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr2:11919800-11924800	Strong transcription	NHDF-Ad	bronchial
38	chr2:11919800-11925000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:11919800-11925000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:11919800-11925000	Strong transcription	Ovary	ovary
41	chr2:11919800-11930000	Strong transcription	Thymus	Thymus
42	chr2:11919800-11933600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:11919800-11934400	Strong transcription	K562	blood
44	chr2:11919800-11937600	Strong transcription	HepG2	liver
45	chr2:11919800-11939600	Strong transcription	Fetal Thymus	thymus
46	chr2:11919800-11940000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:11919800-11940000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:11919800-11940400	Strong transcription	Dnd41	blood
49	chr2:11919800-11940600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr2:11919800-11940600	Strong transcription	Placenta	Placenta

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