Variant report

Variant	rs772160
Chromosome Location	chr2:97039666-97039667
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96999598..97002888-chr2:97039436..97041804,3	K562	blood:
2	chr2:97031285..97033071-chr2:97037029..97039900,2	K562	blood:
3	chr2:97037773..97040106-chr2:97040749..97042480,2	MCF-7	breast:
4	chr2:96999897..97002755-chr2:97039436..97042284,2	K562	blood:
5	chr2:97032551..97034623-chr2:97038174..97040150,2	MCF-7	breast:
6	chr2:96970065..96972935-chr2:97039577..97041922,2	K562	blood:

Variant related genes	Relation type
ENSG00000144028	Chromatin interaction
ENSG00000121152	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1081717	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2438709	1.00[CHD][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap]
rs4907304	1.00[CHD][hapmap];0.82[GIH][hapmap]
rs582014	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs583705	0.85[EUR][1000 genomes]
rs596069	0.88[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs597420	0.83[EUR][1000 genomes]
rs611943	0.83[EUR][1000 genomes]
rs631746	0.91[EUR][1000 genomes]
rs655101	0.80[EUR][1000 genomes]
rs674920	0.91[EUR][1000 genomes]
rs675239	0.81[EUR][1000 genomes]
rs676007	0.81[EUR][1000 genomes]
rs687950	0.85[EUR][1000 genomes]
rs772156	0.92[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs772159	0.96[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs772161	0.91[EUR][1000 genomes]
rs772167	0.81[EUR][1000 genomes]
rs772173	0.92[CEU][hapmap];0.84[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs772174	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs772177	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv819311	chr2:97039430-97039715	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs772160	KIAA1310	cis	cerebellum	SCAN
rs772160	ADRA2B	cis	cerebellum	SCAN
rs772160	ITPRIPL1	cis	Esophagus Mucosa	GTEx
rs772160	LOC285033	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97002800-97040000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:97004000-97040400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:97004200-97040400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:97006200-97041000	Strong transcription	Dnd41	blood
5	chr2:97006600-97040200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:97006600-97040400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:97006800-97040400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:97006800-97040600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:97006800-97040800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:97007000-97040600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:97007200-97040000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:97007200-97040200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:97007200-97040400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:97007200-97041600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:97007400-97040200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr2:97007400-97040400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:97007400-97040600	Strong transcription	Thymus	Thymus
18	chr2:97012600-97040000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:97013800-97040000	Weak transcription	Esophagus	oesophagus
20	chr2:97014800-97040600	Strong transcription	A549	lung
21	chr2:97017000-97040000	Weak transcription	Fetal Kidney	kidney
22	chr2:97019200-97040600	Strong transcription	Fetal Thymus	thymus
23	chr2:97019200-97042000	Weak transcription	Spleen	Spleen
24	chr2:97020000-97041400	Weak transcription	HSMM	muscle
25	chr2:97024400-97040000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:97024600-97040000	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr2:97024800-97039800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:97024800-97039800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr2:97024800-97040000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr2:97028000-97040000	Strong transcription	HepG2	liver
31	chr2:97029000-97041000	Weak transcription	Primary T cells from cord blood	blood
32	chr2:97030000-97040000	Strong transcription	NHEK	skin
33	chr2:97032000-97039800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:97032200-97041800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:97034400-97040600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:97034400-97040600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:97035600-97040000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:97035600-97040000	Weak transcription	NH-A	brain
39	chr2:97036000-97039800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:97036000-97039800	Weak transcription	Brain Substantia Nigra	brain
41	chr2:97036200-97044600	Weak transcription	Gastric	stomach
42	chr2:97036400-97041000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:97036600-97043000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:97036800-97039800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:97037000-97039800	Weak transcription	Stomach Mucosa	stomach
46	chr2:97037000-97040000	Weak transcription	Fetal Brain Female	brain
47	chr2:97037000-97041400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:97037200-97040800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:97037400-97039800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:97037400-97040000	Weak transcription	Placenta	Placenta

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