Variant report

Variant	rs9829896
Chromosome Location	chr3:20177472-20177473
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:19987745..19989859-chr3:20175809..20177957,2	K562	blood:
2	chr3:20080018..20082340-chr3:20176608..20178833,2	K562	blood:

Variant related genes	Relation type
ENSG00000144566	Chromatin interaction
ENSG00000114166	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10048973	0.88[JPT][hapmap]
rs11128936	1.00[JPT][hapmap]
rs1610186	0.88[JPT][hapmap]
rs2293139	1.00[JPT][hapmap]
rs2661376	1.00[JPT][hapmap]
rs2661377	1.00[JPT][hapmap]
rs2661378	0.84[MEX][hapmap]
rs2686315	1.00[JPT][hapmap]
rs2686317	0.84[MEX][hapmap]
rs2929403	1.00[JPT][hapmap]
rs4435663	0.89[MEX][hapmap]
rs977162	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking 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 miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
13	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	esv3394910	chr3:20150394-20203576	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
16	esv3334928	chr3:20150414-20203546	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
17	esv1832674	chr3:20152772-20605302	Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription 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 miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	esv1831853	chr3:20157077-20615273	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	esv1833208	chr3:20157077-20638228	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
20	esv2422249	chr3:20163608-20626956	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
21	esv1826144	chr3:20164282-20638228	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
22	nsv1013532	chr3:20172889-20305612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
23	nsv536513	chr3:20172889-20305612	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9829896	RPL15	cis	parietal	SCAN
rs9829896	KAT2B	cis	cerebellum	SCAN
rs9829896	RAB5A	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
2	chr3:20141200-20222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:20142600-20189400	Weak transcription	Fetal Brain Male	brain
4	chr3:20147600-20194200	Weak transcription	Dnd41	blood
5	chr3:20151000-20196800	Weak transcription	Stomach Mucosa	stomach
6	chr3:20151200-20179000	Weak transcription	Fetal Kidney	kidney
7	chr3:20152000-20182800	Weak transcription	Colonic Mucosa	Colon
8	chr3:20154000-20178400	Weak transcription	Psoas Muscle	Psoas
9	chr3:20157000-20178800	Weak transcription	HUVEC	blood vessel
10	chr3:20159200-20201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:20160400-20182000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:20162200-20183400	Weak transcription	Gastric	stomach
13	chr3:20162200-20184000	Weak transcription	Right Ventricle	heart
14	chr3:20162800-20183000	Weak transcription	Fetal Heart	heart
15	chr3:20162800-20198200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:20164400-20204400	Weak transcription	Small Intestine	intestine
17	chr3:20164800-20181600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:20164800-20181600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:20164800-20211400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:20165000-20178400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:20166200-20178400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:20167800-20181800	Weak transcription	Lung	lung
23	chr3:20167800-20196600	Weak transcription	K562	blood
24	chr3:20167800-20226000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:20168000-20183600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:20168600-20182800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:20168800-20200800	Weak transcription	GM12878-XiMat	blood
28	chr3:20169400-20180800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:20169400-20184400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:20169600-20178400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:20169600-20179000	Weak transcription	Esophagus	oesophagus
32	chr3:20169600-20181800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:20169600-20181800	Weak transcription	Ovary	ovary
34	chr3:20169600-20182000	Weak transcription	Fetal Intestine Small	intestine
35	chr3:20169600-20182000	Weak transcription	Spleen	Spleen
36	chr3:20169600-20182400	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:20169600-20182600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:20169600-20183400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:20169600-20183400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:20169600-20189600	Weak transcription	Fetal Intestine Large	intestine
41	chr3:20169600-20189600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:20169600-20198400	Weak transcription	Aorta	Aorta
43	chr3:20169600-20198400	Weak transcription	Pancreas	Pancrea
44	chr3:20169800-20178400	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:20169800-20178400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:20169800-20179000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:20169800-20179000	Weak transcription	Fetal Stomach	stomach
48	chr3:20169800-20182400	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:20169800-20183600	Weak transcription	Brain Angular Gyrus	brain
50	chr3:20169800-20201600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links