Variant report

Variant	rs4668676
Chromosome Location	chr2:10438621-10438622
allele	A/C
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	TCF12	chr2:10437872-10438742	SK-N-SH	brain:	n/a	n/a
2	NR2F2	chr2:10437904-10438708	K562	blood:	n/a	n/a
3	FOS	chr2:10437817-10438654	HUVEC	blood vessel:	n/a	chr2:10438159-10438170 chr2:10438163-10438171 chr2:10438161-10438172
4	MAZ	chr2:10437642-10438833	IMR90	lung:	n/a	n/a
5	RCOR1	chr2:10437395-10439303	IMR90	lung:	n/a	n/a
6	GATA3	chr2:10437899-10438642	SK-N-SH	brain:	n/a	chr2:10438164-10438173
7	MXI1	chr2:10437472-10439115	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr2:10437953-10438719	U87	brain:	n/a	n/a
9	RXRA	chr2:10437890-10438739	SK-N-SH	brain:	n/a	chr2:10438435-10438451 chr2:10438476-10438495
10	MAX	chr2:10437911-10438843	A549	lung:	n/a	n/a
11	CBX3	chr2:10437768-10438646	K562	blood:	n/a	n/a
12	FOSL1	chr2:10437746-10438646	HCT-116	colon:	n/a	chr2:10438159-10438170 chr2:10438163-10438171 chr2:10438161-10438172
13	JUND	chr2:10437148-10438905	SK-N-SH	brain:	n/a	chr2:10438159-10438170 chr2:10438163-10438171
14	JUND	chr2:10437796-10438735	HCT-116	colon:	n/a	chr2:10438159-10438170 chr2:10438163-10438171
15	EP300	chr2:10437795-10438625	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr2:10437947-10438725	U87	brain:	n/a	n/a
17	SP1	chr2:10437744-10438657	HCT-116	colon:	n/a	chr2:10438132-10438142 chr2:10438132-10438141 chr2:10438077-10438086
18	JUN	chr2:10438019-10439025	K562	blood:	n/a	chr2:10438159-10438170 chr2:10438163-10438171
19	TCF12	chr2:10437785-10438714	SK-N-SH	brain:	n/a	n/a
20	EP300	chr2:10437422-10439314	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10405314..10407272-chr2:10438185..10440055,2	K562	blood:
2	chr2:10438477..10441704-chr2:10442402..10444544,4	MCF-7	breast:
3	chr2:10423331..10426574-chr2:10438305..10440403,3	K562	blood:
4	chr2:10437138..10439470-chr2:10586145..10589513,3	K562	blood:
5	chr2:10425416..10427502-chr2:10437383..10439645,2	K562	blood:
6	chr2:10409808..10412548-chr2:10436886..10439745,2	K562	blood:
7	chr2:10434745..10440361-chr2:10440769..10446494,13	MCF-7	breast:
8	chr2:10436760..10438833-chr2:10575893..10578796,2	K562	blood:
9	chr2:10436642..10438745-chr2:10547775..10550649,2	K562	blood:

Variant related genes	Relation type
ENSG00000206898	TF binding region
HPCAL1	TF binding region
ENSG00000115756	Chromatin interaction
ENSG00000257135	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000115758	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2192670	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2884208	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs62128554	0.86[ASN][1000 genomes]
rs6432090	0.82[ASN][1000 genomes]
rs6432091	0.82[JPT][hapmap];0.81[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	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873639	chr2:10372061-10475308	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers 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
3	esv19004	chr2:10433505-10439183	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4668676	PDIA6	cis	parietal	SCAN
rs4668676	IAH1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10435200-10438800	Enhancers	Placenta	Placenta
2	chr2:10435800-10441000	Weak transcription	Stomach Mucosa	stomach
3	chr2:10436000-10442000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:10436600-10442200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:10437000-10438800	Enhancers	Fetal Thymus	thymus
6	chr2:10437000-10439000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:10437200-10438800	Enhancers	K562	blood
8	chr2:10437400-10438800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:10437400-10438800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr2:10437400-10438800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr2:10437400-10438800	Enhancers	HMEC	breast
12	chr2:10437400-10439000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:10437400-10439000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr2:10437400-10439000	Enhancers	Hela-S3	cervix
15	chr2:10437400-10439600	Enhancers	Primary B cells from cord blood	blood
16	chr2:10437600-10438800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr2:10437600-10438800	Enhancers	Primary T cells from cord blood	blood
18	chr2:10437600-10438800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:10437600-10438800	Enhancers	Fetal Muscle Leg	muscle
20	chr2:10437600-10438800	Enhancers	NHDF-Ad	bronchial
21	chr2:10437600-10438800	Enhancers	NHEK	skin
22	chr2:10437600-10438800	Enhancers	NHLF	lung
23	chr2:10437600-10439000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:10437600-10439000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr2:10437600-10439000	Enhancers	NH-A	brain
26	chr2:10437600-10440600	Enhancers	HepG2	liver
27	chr2:10437800-10438800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:10437800-10438800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:10437800-10438800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:10437800-10438800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr2:10437800-10438800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:10437800-10438800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:10437800-10438800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:10437800-10438800	Enhancers	Osteobl	bone
35	chr2:10437800-10439000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr2:10437800-10439000	Enhancers	HUVEC	blood vessel
37	chr2:10437800-10439000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr2:10437800-10439200	Enhancers	Primary B cells from peripheral blood	blood
39	chr2:10437800-10439200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr2:10437800-10441600	Weak transcription	Spleen	Spleen
41	chr2:10437800-10441800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:10438200-10438800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr2:10438200-10438800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr2:10438200-10438800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:10438200-10438800	Enhancers	HSMMtube	muscle
46	chr2:10438400-10438800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr2:10438400-10438800	Enhancers	Liver	Liver
48	chr2:10438400-10438800	Enhancers	Colon Smooth Muscle	Colon
49	chr2:10438400-10439000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:10438400-10439600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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