Variant report

Variant	rs7863139
Chromosome Location	chr9:15477387-15477388
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	POLR2A	chr9:15477195-15477443	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:15473884-15478044	K562	blood:	n/a	n/a
3	POLR2A	chr9:15477338-15477538	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15422994..15424695-chr9:15475354..15478030,2	K562	blood:

Variant related genes	Relation type
PSIP1	TF binding region
ENSG00000164975	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10283923	0.96[ASN][1000 genomes]
rs10283927	0.96[ASN][1000 genomes]
rs12336503	0.96[ASN][1000 genomes]
rs12336509	0.96[ASN][1000 genomes]
rs12339417	0.96[ASN][1000 genomes]
rs12683553	0.96[ASN][1000 genomes]
rs12686545	0.93[ASN][1000 genomes]
rs16933296	0.80[EUR][1000 genomes]
rs16933311	1.00[ASN][1000 genomes]
rs16933320	0.93[ASN][1000 genomes]
rs16933348	0.91[ASN][1000 genomes]
rs16933350	0.80[EUR][1000 genomes]
rs1828382	0.87[EUR][1000 genomes]
rs1828383	0.81[ASN][1000 genomes]
rs2175257	0.96[ASN][1000 genomes]
rs2277191	0.89[ASN][1000 genomes]
rs2777950	0.98[ASN][1000 genomes]
rs28537229	0.83[ASN][1000 genomes]
rs3087653	0.85[EUR][1000 genomes]
rs41268961	0.85[EUR][1000 genomes]
rs41306098	0.85[EUR][1000 genomes]
rs55771541	0.87[ASN][1000 genomes]
rs56361298	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57142629	0.87[EUR][1000 genomes]
rs57191285	0.91[EUR][1000 genomes]
rs57467578	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57849124	0.91[EUR][1000 genomes]
rs58607272	0.81[ASN][1000 genomes]
rs58915725	0.87[EUR][1000 genomes]
rs59520337	0.80[EUR][1000 genomes]
rs59639757	0.87[ASN][1000 genomes]
rs62570980	0.85[EUR][1000 genomes]
rs62570991	0.85[EUR][1000 genomes]
rs62570992	0.85[EUR][1000 genomes]
rs62570993	0.85[EUR][1000 genomes]
rs62571001	0.80[EUR][1000 genomes]
rs62571002	0.80[EUR][1000 genomes]
rs62571003	0.82[EUR][1000 genomes]
rs62571007	0.85[EUR][1000 genomes]
rs62571008	0.82[EUR][1000 genomes]
rs62571009	0.85[EUR][1000 genomes]
rs62571010	0.96[ASN][1000 genomes]
rs62571011	0.85[EUR][1000 genomes]
rs62571018	0.80[EUR][1000 genomes]
rs62571021	0.91[EUR][1000 genomes]
rs62571022	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62571023	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62571024	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62571027	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62571029	0.80[EUR][1000 genomes]
rs62571031	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62571032	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7018658	0.96[ASN][1000 genomes]
rs7021153	0.82[ASN][1000 genomes]
rs7023730	0.87[EUR][1000 genomes]
rs73408328	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73408340	0.91[EUR][1000 genomes]
rs7856710	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7857933	0.89[ASN][1000 genomes]
rs7863046	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7863139	PSIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15433400-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:15439000-15492200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:15442600-15478200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr9:15442600-15478600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:15442800-15508400	Strong transcription	Fetal Thymus	thymus
6	chr9:15443000-15478000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr9:15443000-15482200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:15443200-15478000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr9:15443200-15479600	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr9:15443200-15490400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:15443200-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:15443400-15479200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr9:15443800-15492200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:15444000-15482000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:15444000-15487600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:15444000-15492400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:15444400-15495200	Weak transcription	Fetal Heart	heart
18	chr9:15444600-15491200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:15444800-15482200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:15447000-15509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:15448200-15482200	Weak transcription	Psoas Muscle	Psoas
22	chr9:15448400-15480000	Weak transcription	Stomach Mucosa	stomach
23	chr9:15449000-15492200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:15449800-15478000	Strong transcription	Fetal Lung	lung
25	chr9:15449800-15509000	Weak transcription	Small Intestine	intestine
26	chr9:15452200-15480200	Weak transcription	Brain Substantia Nigra	brain
27	chr9:15452200-15492400	Weak transcription	Right Ventricle	heart
28	chr9:15454200-15478600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:15454600-15508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:15456200-15480600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:15457000-15482000	Strong transcription	Dnd41	blood
32	chr9:15457000-15492400	Weak transcription	Lung	lung
33	chr9:15458200-15478200	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr9:15459000-15492200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr9:15460800-15510000	Weak transcription	Esophagus	oesophagus
36	chr9:15461000-15492200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:15461400-15478000	Strong transcription	Primary B cells from cord blood	blood
38	chr9:15461600-15483800	Weak transcription	Fetal Intestine Small	intestine
39	chr9:15461600-15492400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:15461600-15492800	Weak transcription	Pancreas	Pancrea
41	chr9:15462200-15482200	Weak transcription	Brain Angular Gyrus	brain
42	chr9:15462400-15478600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr9:15462800-15505200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:15463800-15478600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr9:15466200-15492400	Weak transcription	Gastric	stomach
46	chr9:15466600-15492400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:15467200-15501000	Weak transcription	Colon Smooth Muscle	Colon
48	chr9:15467400-15505600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:15468800-15480600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr9:15468800-15482800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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