Variant report

Variant	rs11690125
Chromosome Location	chr2:11940171-11940172
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	chr2:11939618-11941828	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr2:11940028-11940617	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11936274..11938769-chr2:11939314..11940950,2	K562	blood:
2	chr2:11939347..11940911-chr2:11941287..11943007,2	K562	blood:

Variant related genes	Relation type
LPIN1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10520097	0.93[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11679358	0.93[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11694797	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11695081	0.93[CEU][hapmap]
rs11695610	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13412852	1.00[ASW][hapmap]
rs17603197	1.00[ASW][hapmap];0.81[CEU][hapmap];0.83[MEX][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs17603755	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2358042	1.00[ASW][hapmap]
rs2358125	0.86[AMR][1000 genomes]
rs3762583	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4129758	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62113359	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62114960	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7587836	0.83[MEX][hapmap]

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
rs11690125	FAM84A	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11916800-11961200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:11919400-11940400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:11919400-11943400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:11919400-11961800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:11919600-11940800	Strong transcription	Left Ventricle	heart
6	chr2:11919600-11940800	Strong transcription	NHEK	skin
7	chr2:11919600-11968400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:11919800-11940400	Strong transcription	Dnd41	blood
9	chr2:11919800-11940600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr2:11919800-11940600	Strong transcription	Placenta	Placenta
11	chr2:11919800-11948400	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:11919800-11949000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:11919800-11957600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:11919800-11957800	Strong transcription	Primary T cells from cord blood	blood
15	chr2:11919800-11959200	Strong transcription	Liver	Liver
16	chr2:11919800-11960400	Weak transcription	Stomach Mucosa	stomach
17	chr2:11919800-11963200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr2:11919800-11967600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:11919800-11968400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:11919800-11968800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:11920000-11940400	Strong transcription	HMEC	breast
22	chr2:11920000-11941000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr2:11920200-11940800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:11920400-11940400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:11920400-11940400	Strong transcription	Gastric	stomach
26	chr2:11924600-11947800	Weak transcription	Right Atrium	heart
27	chr2:11925200-11940200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr2:11925200-11941000	Strong transcription	Ovary	ovary
29	chr2:11925200-11949400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr2:11925200-11964800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:11925200-11968600	Strong transcription	NHLF	lung
32	chr2:11925400-11940800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr2:11925600-11940400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:11925600-11940600	Strong transcription	Brain Hippocampus Middle	brain
35	chr2:11925600-11946400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:11925800-11968600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:11926200-11948600	Strong transcription	Primary hematopoietic stem cells	blood
38	chr2:11926400-11940400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:11926600-11941200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr2:11926800-11940400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:11928400-11948800	Strong transcription	HUVEC	blood vessel
42	chr2:11929600-11944600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:11929800-11947000	Weak transcription	Fetal Heart	heart
44	chr2:11929800-11951200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:11929800-11955200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:11931400-11940200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:11931800-11940400	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr2:11931800-11940400	Strong transcription	Right Ventricle	heart
49	chr2:11931800-11940600	Strong transcription	Esophagus	oesophagus
50	chr2:11931800-11940600	Strong transcription	Fetal Muscle Leg	muscle

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