Variant report

Variant	rs3176774
Chromosome Location	chr12:9917106-9917107
allele	G/T
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	BRCA1	chr12:9917019-9917219	GM12878	blood:	n/a	n/a
2	RCOR1	chr12:9916803-9918075	GM12878	blood:	n/a	n/a
3	GATA1	chr12:9916592-9918259	PBDE	blood:	n/a	chr12:9918194-9918207 chr12:9917534-9917550 chr12:9917539-9917556
4	NFE2	chr12:9917078-9917128	GM12878	blood:	n/a	n/a
5	MAX	chr12:9916412-9918022	NB4	blood:	n/a	chr12:9916589-9916599
6	IRF1	chr12:9917030-9917832	K562	blood:	n/a	n/a
7	STAT3	chr12:9916518-9918102	GM12878	blood:	n/a	chr12:9917753-9917761 chr12:9917226-9917237
8	KAP1	chr12:9916865-9917788	K562	blood:	n/a	n/a
9	POLR2A	chr12:9917081-9917834	K562	blood:	n/a	n/a
10	NFIC	chr12:9917089-9918246	GM12878	blood:	n/a	n/a
11	JUN	chr12:9917054-9917720	K562	blood:	n/a	n/a
12	CUX1	chr12:9916645-9918269	GM12878	blood:	n/a	chr12:9916944-9916953
13	ELK1	chr12:9917090-9917747	K562	blood:	n/a	n/a
14	POLR2A	chr12:9916528-9918291	PBDE	blood:	n/a	n/a
15	POLR2A	chr12:9916819-9918098	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:9916802-9918147	GM12878	blood:	n/a	n/a
17	NFIC	chr12:9917025-9918134	GM12878	blood:	n/a	n/a
18	TBL1XR1	chr12:9916464-9918325	GM12878	blood:	n/a	n/a
19	ATF2	chr12:9917106-9918080	GM12878	blood:	n/a	n/a
20	RELA	chr12:9917034-9918126	GM10847	blood:	n/a	chr12:9917852-9917861 chr12:9917852-9917861
21	MXI1	chr12:9917093-9918127	GM12878	blood:	n/a	n/a
22	ZNF384	chr12:9916366-9917112	GM12878	blood:	n/a	n/a
23	RELA	chr12:9916566-9918311	GM12878	blood:	n/a	chr12:9917852-9917861 chr12:9917852-9917861
24	EP300	chr12:9916500-9918141	GM12878	blood:	n/a	chr12:9917638-9917652 chr12:9917636-9917650
25	ELK1	chr12:9916591-9918099	GM12878	blood:	n/a	n/a
26	MAZ	chr12:9916671-9918015	GM12878	blood:	n/a	n/a
27	RELA	chr12:9916986-9918134	GM18951	blood:	n/a	chr12:9917852-9917861 chr12:9917852-9917861
28	MYC	chr12:9916415-9917807	K562	blood:	n/a	chr12:9916589-9916599
29	EP300	chr12:9916507-9918107	GM12878	blood:	n/a	chr12:9917638-9917652 chr12:9917636-9917650
30	POLR2A	chr12:9916807-9918133	GM12878	blood:	n/a	n/a
31	JUN	chr12:9917104-9918483	K562	blood:	n/a	n/a
32	BHLHE40	chr12:9916982-9917903	K562	blood:	n/a	n/a
33	IRF1	chr12:9916943-9917866	K562	blood:	n/a	n/a
34	MYC	chr12:9917062-9917835	NB4	blood:	n/a	n/a
35	TBP	chr12:9916582-9918161	GM12878	blood:	n/a	n/a
36	TBL1XR1	chr12:9916549-9918061	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9916372..9918378-chr12:9944960..9947867,2	K562	blood:
2	chr12:9895231..9897767-chr12:9915766..9917544,2	K562	blood:
3	chr12:9916166..9917917-chr12:9948178..9949717,2	K562	blood:

Variant related genes	Relation type
CD69	TF binding region

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs7316342	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7966093	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[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	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv975645	chr12:9917034-9924808	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3176774	C1RL	cis	parietal	SCAN
rs3176774	ING4	cis	cerebellum	SCAN
rs3176774	PZP	cis	cerebellum	SCAN
rs3176774	DCAL1	cis	multi-tissue	Pritchard
rs3176774	GPR19	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9903400-9917600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:9913800-9917600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr12:9914200-9917400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr12:9914200-9917800	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr12:9914200-9918600	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:9914400-9917400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr12:9914400-9918400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr12:9914400-9918600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:9914600-9917800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:9914600-9918400	Enhancers	Fetal Thymus	thymus
11	chr12:9914600-9918600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:9914600-9920200	Enhancers	Primary T cells from cord blood	blood
13	chr12:9914800-9918600	Enhancers	Primary hematopoietic stem cells	blood
14	chr12:9915600-9917200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr12:9916000-9917800	Enhancers	K562	blood
16	chr12:9916000-9918400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr12:9916200-9918400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:9916400-9917200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:9916400-9917400	Enhancers	Fetal Intestine Small	intestine
20	chr12:9916400-9917400	Flanking Active TSS	GM12878-XiMat	blood
21	chr12:9916600-9917400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr12:9916600-9918000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:9916600-9918400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:9916800-9917200	Enhancers	Duodenum Mucosa	Duodenum
25	chr12:9916800-9917400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr12:9916800-9917400	Flanking Active TSS	Thymus	Thymus
27	chr12:9916800-9917400	Flanking Active TSS	Dnd41	blood
28	chr12:9917000-9917200	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr12:9917000-9917200	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr12:9917000-9917200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:9917000-9917400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:9917000-9917400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr12:9917000-9917800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr12:9917000-9918200	Enhancers	HUVEC	blood vessel

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