Variant report

Variant	rs788163
Chromosome Location	chr2:172931559-172931560
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr2:172931185-172931584	K562	blood:	n/a	n/a
2	POLR2A	chr2:172931013-172931724	H1-neurons	neurons:	n/a	n/a
3	TAL1	chr2:172931193-172931564	K562	blood:	n/a	n/a
4	RCOR1	chr2:172931013-172931617	K562	blood:	n/a	n/a
5	ZMIZ1	chr2:172931206-172931584	K562	blood:	n/a	n/a
6	ZNF384	chr2:172931425-172931634	K562	blood:	n/a	n/a
7	EP300	chr2:172931166-172931584	K562	blood:	n/a	chr2:172931358-172931374 chr2:172931294-172931301
8	POLR2A	chr2:172931006-172931694	H1-neurons	neurons:	n/a	n/a
9	CTCF	chr2:172931228-172931613	K562	blood:	n/a	n/a
10	ATF1	chr2:172931142-172931636	K562	blood:	n/a	n/a
11	TEAD4	chr2:172931110-172931670	K562	blood:	n/a	n/a
12	JUND	chr2:172931160-172931669	K562	blood:	n/a	n/a
13	MAFK	chr2:172931543-172931705	K562	blood:	n/a	n/a
14	CUX1	chr2:172931075-172931708	K562	blood:	n/a	n/a
15	REST	chr2:172931325-172931624	K562	blood:	n/a	n/a
16	REST	chr2:172931386-172931581	K562	blood:	n/a	n/a
17	TEAD4	chr2:172931108-172931672	K562	blood:	n/a	n/a
18	CHD2	chr2:172931496-172931656	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172929662..172931943-chr2:172933111..172935492,3	MCF-7	breast:
2	chr2:172930135..172933791-chr2:172934281..172936934,5	K562	blood:

No data

Variant related genes	Relation type
METAP1D	TF binding region
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1008151	0.88[YRI][hapmap]
rs1008152	0.85[EUR][1000 genomes]
rs13020884	0.88[YRI][hapmap]
rs1965160	0.81[YRI][hapmap]
rs55791993	0.85[EUR][1000 genomes]
rs62183852	0.86[EUR][1000 genomes]
rs6737876	0.86[EUR][1000 genomes]
rs705870	0.95[CEU][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs788161	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs788164	0.90[CEU][hapmap];0.86[MEX][hapmap]
rs788166	0.96[YRI][hapmap]
rs788168	0.90[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[EUR][1000 genomes]
rs788170	0.96[YRI][hapmap]
rs788171	0.86[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][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	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv875412	chr2:172903124-172942448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs788163	DHRS9	cis	parietal	SCAN
rs788163	METTL8	cis	cerebellum	SCAN
rs788163	DYNC1I2	cis	parietal	SCAN
rs788163	BBS5	cis	cerebellum	SCAN
rs788163	DCAF17	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172911200-172947200	Weak transcription	HSMM	muscle
2	chr2:172914000-172937000	Weak transcription	Pancreas	Pancrea
3	chr2:172917400-172934800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:172917800-172932000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:172917800-172944800	Weak transcription	Brain Substantia Nigra	brain
6	chr2:172918000-172932800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:172918600-172935600	Weak transcription	Fetal Kidney	kidney
8	chr2:172918600-172935800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:172921800-172937200	Weak transcription	HepG2	liver
10	chr2:172923600-172939800	Weak transcription	Psoas Muscle	Psoas
11	chr2:172924200-172935800	Weak transcription	Adipose Nuclei	Adipose
12	chr2:172925600-172932400	Weak transcription	Dnd41	blood
13	chr2:172925800-172937200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:172925800-172937400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:172925800-172942400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:172926000-172932000	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:172926200-172933200	Weak transcription	Aorta	Aorta
18	chr2:172926200-172933400	Weak transcription	Right Ventricle	heart
19	chr2:172926400-172935200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:172926600-172933400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:172927000-172933800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:172927200-172931600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:172927200-172941600	Weak transcription	Gastric	stomach
24	chr2:172927600-172933200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:172927600-172933400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:172927800-172936800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:172928200-172935800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:172928400-172932200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:172928400-172932600	Weak transcription	Fetal Heart	heart
30	chr2:172928600-172933600	Weak transcription	Spleen	Spleen
31	chr2:172928600-172937400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:172928600-172940000	Weak transcription	Left Ventricle	heart
33	chr2:172929000-172933000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:172929400-172933400	Weak transcription	GM12878-XiMat	blood
35	chr2:172930000-172931600	Strong transcription	Primary T cells from cord blood	blood
36	chr2:172930000-172932800	Weak transcription	Brain Anterior Caudate	brain
37	chr2:172930000-172933000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:172930200-172933600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:172930200-172933800	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:172931000-172931600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:172931000-172931600	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr2:172931000-172931600	Strong transcription	Ovary	ovary
43	chr2:172931000-172931600	Enhancers	HSMMtube	muscle
44	chr2:172931000-172931800	Enhancers	K562	blood
45	chr2:172931400-172931600	Strong transcription	Primary B cells from cord blood	blood
46	chr2:172931400-172931600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:172931400-172931600	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links