Variant report

Variant	rs12122361
Chromosome Location	chr1:174933414-174933415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr1:174933404-174935094	PBDE	blood:	n/a	chr1:174934268-174934277
2	NR2F2	chr1:174933331-174934067	K562	blood:	n/a	n/a
3	IRF1	chr1:174933280-174935009	K562	blood:	n/a	chr1:174933549-174933563
4	SMARCB1	chr1:174932813-174935258	K562	blood:	n/a	n/a
5	NR2F2	chr1:174932392-174935014	K562	blood:	n/a	n/a
6	CEBPB	chr1:174933397-174934070	K562	blood:	n/a	n/a
7	TBP	chr1:174933400-174934441	K562	blood:	n/a	n/a
8	CCNT2	chr1:174933332-174934608	K562	blood:	n/a	n/a
9	MAX	chr1:174933339-174934002	NB4	blood:	n/a	n/a
10	TBL1XR1	chr1:174933312-174933899	K562	blood:	n/a	n/a
11	HMGN3	chr1:174933311-174933954	K562	blood:	n/a	n/a
12	CUX1	chr1:174933395-174935192	K562	blood:	n/a	n/a
13	TEAD4	chr1:174933338-174935083	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:174932689..174934966-chr1:174943606..174946963,3	K562	blood:
2	chr1:174927580..174945830-chr1:174955726..174971213,32	K562	blood:
3	chr1:174932418..174935374-chr1:174964535..174970014,5	K562	blood:

No data

Variant related genes	Relation type
RABGAP1L	TF binding region
ENSG00000116161	Chromatin interaction
ENSG00000152061	Chromatin interaction
ENSG00000252552	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10912860	1.00[CHB][hapmap]
rs10912867	0.96[TSI][hapmap]
rs12122399	1.00[CHB][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap]
rs12123868	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126129	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691857	1.00[CHB][hapmap]
rs6700816	1.00[CHB][hapmap]
rs7537508	1.00[CHB][hapmap];0.96[TSI][hapmap]
rs7550448	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12122361	RC3H1	Cis_1M	lymphoblastoid	RTeQTL
rs12122361	PRDX6	cis	cerebellum	SCAN
rs12122361	GPR52	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
3	chr1:174910800-174957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:174912600-174934800	Weak transcription	Left Ventricle	heart
5	chr1:174923000-174933600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:174924000-174933800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:174924000-174938200	Weak transcription	Psoas Muscle	Psoas
8	chr1:174924200-174967800	Weak transcription	Brain Germinal Matrix	brain
9	chr1:174924400-174933600	Weak transcription	Fetal Kidney	kidney
10	chr1:174924400-174958200	Weak transcription	Fetal Brain Male	brain
11	chr1:174925000-174933600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:174925000-174934400	Weak transcription	Pancreas	Pancrea
13	chr1:174925000-174940800	Weak transcription	Gastric	stomach
14	chr1:174927800-174934400	Weak transcription	Right Atrium	heart
15	chr1:174928000-174933800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:174928000-174934200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:174928000-174938200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:174928200-174933600	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:174928200-174933600	Weak transcription	Brain Substantia Nigra	brain
20	chr1:174928400-174934200	Weak transcription	Brain Angular Gyrus	brain
21	chr1:174928800-174933600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:174928800-174933800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:174929600-174933600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:174930200-174933600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:174930400-174933800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:174930800-174934200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:174930800-174937800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:174931800-174935200	Enhancers	GM12878-XiMat	blood
29	chr1:174932000-174933600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:174932000-174933600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:174932000-174933800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr1:174932000-174934000	Enhancers	Dnd41	blood
33	chr1:174932000-174938400	Enhancers	Fetal Intestine Small	intestine
34	chr1:174932200-174933600	Enhancers	Primary T cells from cord blood	blood
35	chr1:174932200-174933600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:174932200-174933600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr1:174932200-174933800	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr1:174932200-174934000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:174932400-174933600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:174932400-174933600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr1:174932400-174933600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr1:174932400-174933600	Enhancers	Colon Smooth Muscle	Colon
43	chr1:174932400-174933600	Enhancers	HSMMtube	muscle
44	chr1:174932400-174933800	Enhancers	Primary T cells fromperipheralblood	blood
45	chr1:174932400-174933800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr1:174932400-174933800	Enhancers	Adipose Nuclei	Adipose
47	chr1:174932400-174934200	Enhancers	Liver	Liver
48	chr1:174932400-174934200	Enhancers	Duodenum Mucosa	Duodenum
49	chr1:174932400-174934600	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr1:174932400-174935000	Enhancers	Hela-S3	cervix

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