Variant report

Variant	rs4669123
Chromosome Location	chr2:7116077-7116078
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	NFIC	chr2:7116040-7116698	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr2:7116076-7116674	ECC-1	luminal epithelium:	n/a	n/a
3	FOS	chr2:7116051-7116570	HUVEC	blood vessel:	n/a	n/a
4	CEBPB	chr2:7115943-7116704	HCT-116	colon:	n/a	chr2:7116620-7116633 chr2:7116620-7116633
5	CEBPB	chr2:7116074-7116696	A549	lung:	n/a	chr2:7116620-7116633 chr2:7116620-7116633
6	JUND	chr2:7115967-7116622	HCT-116	colon:	n/a	n/a
7	CEBPB	chr2:7116006-7116692	HCT-116	colon:	n/a	chr2:7116620-7116633 chr2:7116620-7116633
8	STAT3	chr2:7115961-7116554	MCF10A-Er-Src	breast:	n/a	n/a
9	SP1	chr2:7115976-7116518	HCT-116	colon:	n/a	n/a
10	SP1	chr2:7115915-7116664	HCT-116	colon:	n/a	n/a
11	MAX	chr2:7116052-7116570	HCT-116	colon:	n/a	n/a
12	EGR1	chr2:7116058-7116644	HCT-116	colon:	n/a	n/a
13	JUND	chr2:7115938-7116607	HCT-116	colon:	n/a	n/a
14	FOSL1	chr2:7115937-7116708	HCT-116	colon:	n/a	n/a
15	EGR1	chr2:7116026-7116742	HCT-116	colon:	n/a	n/a
16	GATA2	chr2:7115951-7116636	HUVEC	blood vessel:	n/a	n/a
17	JUN	chr2:7116040-7116531	HUVEC	blood vessel:	n/a	n/a
18	GATA3	chr2:7116029-7116615	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:7113332..7116286-chr2:9136805..9139495,2	MCF-7	breast:

Variant related genes	Relation type
RNF144A	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11685858	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs1448869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1448870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2166967	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34393586	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3771999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772000	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669122	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55736658	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs771254	0.95[JPT][hapmap]
rs771272	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs881938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833326	chr2:6985027-7142564	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv2598	chr2:7088737-7133415	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4669123	TSSC1	cis	parietal	SCAN
rs4669123	ADAM17	cis	cerebellum	SCAN
rs4669123	RNF144A	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7083800-7129600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:7084200-7122200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:7085000-7120200	Weak transcription	Fetal Intestine Small	intestine
4	chr2:7096800-7120600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:7097200-7126200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:7099000-7123600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:7101000-7117400	Weak transcription	Right Atrium	heart
8	chr2:7101000-7130000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:7101200-7117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:7101200-7126200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:7101200-7144000	Weak transcription	Aorta	Aorta
12	chr2:7101200-7154000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:7101400-7117200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:7101600-7117200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:7101800-7126200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr2:7102000-7117400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:7102200-7117400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:7102400-7117000	Weak transcription	Fetal Brain Male	brain
19	chr2:7104200-7120600	Strong transcription	Dnd41	blood
20	chr2:7105600-7120600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:7106200-7123200	Strong transcription	Primary T cells from cord blood	blood
22	chr2:7107200-7117000	Weak transcription	Fetal Lung	lung
23	chr2:7109200-7117400	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:7109200-7137000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:7109400-7117400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:7110600-7120200	Weak transcription	Fetal Thymus	thymus
27	chr2:7111000-7118000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:7111200-7117000	Weak transcription	Brain Germinal Matrix	brain
29	chr2:7111200-7117200	Weak transcription	Fetal Brain Female	brain
30	chr2:7111600-7126400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr2:7111800-7117400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:7111800-7118000	Weak transcription	Right Ventricle	heart
33	chr2:7112000-7116200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:7112000-7118200	Weak transcription	Spleen	Spleen
35	chr2:7112200-7117400	Weak transcription	Adipose Nuclei	Adipose
36	chr2:7112400-7117200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:7112400-7117400	Weak transcription	Psoas Muscle	Psoas
38	chr2:7112400-7117400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:7112400-7122400	Weak transcription	Fetal Kidney	kidney
40	chr2:7112400-7122800	Weak transcription	Ovary	ovary
41	chr2:7112600-7119600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:7113000-7122800	Weak transcription	Lung	lung
43	chr2:7113200-7116400	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:7113400-7120600	Weak transcription	Thymus	Thymus
45	chr2:7113600-7116400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:7113600-7123600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr2:7114000-7118000	Weak transcription	Fetal Stomach	stomach
48	chr2:7114400-7117000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:7114400-7126200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr2:7114600-7117400	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links