Variant report

Variant	rs596069
Chromosome Location	chr2:97076642-97076643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:97075447..97077010-chr2:97171483..97174196,2	MCF-7	breast:
2	chr2:96995918..96997445-chr2:97074228..97076683,2	K562	blood:

Variant related genes	Relation type
ENSG00000163121	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10170018	0.84[AMR][1000 genomes]
rs1081711	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1081713	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2083276	0.84[AMR][1000 genomes]
rs2579502	0.85[MEX][hapmap]
rs2579505	0.88[CEU][hapmap]
rs582014	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs583705	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs585781	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs597420	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs605175	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs607302	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs609765	0.88[AMR][1000 genomes]
rs611943	0.85[EUR][1000 genomes]
rs612017	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs618454	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs631033	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs631746	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs654224	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs655101	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs670498	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs674920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs675239	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs676007	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs679414	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs687950	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs749027	0.85[MEX][hapmap]
rs772156	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs772159	0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs772160	0.88[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs772161	0.89[EUR][1000 genomes]
rs772167	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs772173	0.96[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs772174	0.92[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs772177	0.80[MEX][hapmap];0.93[TSI][hapmap]

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	esv3416952	chr2:97043127-97076830	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs596069	ADRA2B	cis	cerebellum	SCAN
rs596069	ITPRIPL1	cis	Esophagus Mucosa	GTEx
rs596069	LOC285033	cis	parietal	SCAN
rs596069	STARD7	cis	Liver	GTEx
rs596069	KIAA1310	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97073000-97077000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:97073200-97076800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:97073200-97076800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:97073600-97078400	Weak transcription	Esophagus	oesophagus
5	chr2:97073600-97078400	Weak transcription	Psoas Muscle	Psoas
6	chr2:97073800-97078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:97074000-97076800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:97074200-97076800	Enhancers	Spleen	Spleen
9	chr2:97074400-97076800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:97074400-97077400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:97074400-97078200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:97074400-97079400	Weak transcription	Gastric	stomach
13	chr2:97074600-97077000	Enhancers	Brain Germinal Matrix	brain
14	chr2:97074800-97078000	Weak transcription	K562	blood
15	chr2:97074800-97078200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:97074800-97078400	Weak transcription	Right Atrium	heart
17	chr2:97075200-97078400	Weak transcription	Colonic Mucosa	Colon
18	chr2:97075200-97078800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:97075400-97078800	Weak transcription	Aorta	Aorta
20	chr2:97075600-97078400	Weak transcription	Brain Anterior Caudate	brain
21	chr2:97075600-97079000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:97075600-97079400	Weak transcription	Fetal Kidney	kidney
23	chr2:97075800-97078400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:97075800-97078400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:97075800-97079000	Weak transcription	NH-A	brain
26	chr2:97076000-97078400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:97076000-97078400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:97076000-97078400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:97076000-97078400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:97076000-97078400	Weak transcription	HMEC	breast
31	chr2:97076000-97078600	Weak transcription	Brain Angular Gyrus	brain
32	chr2:97076000-97078600	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:97076000-97078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:97076000-97078600	Weak transcription	Brain Substantia Nigra	brain
35	chr2:97076000-97078600	Weak transcription	Fetal Thymus	thymus
36	chr2:97076000-97078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:97076000-97078800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:97076000-97078800	Weak transcription	Ovary	ovary
39	chr2:97076000-97079200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:97076200-97078600	Enhancers	A549	lung
41	chr2:97076200-97079000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:97076200-97079000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:97076400-97078600	Enhancers	Hela-S3	cervix
44	chr2:97076600-97076800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr2:97076600-97076800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:97076600-97076800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr2:97076600-97076800	Flanking Active TSS	Pancreas	Pancrea
48	chr2:97076600-97076800	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr2:97076600-97076800	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr2:97076600-97076800	Flanking Bivalent TSS/Enh	HepG2	liver

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