Variant report

Variant	rs675239
Chromosome Location	chr2:97076556-97076557
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: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1081711	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1081713	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs582014	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs583705	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs585781	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs596069	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs597420	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605175	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs607302	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs609765	0.81[AMR][1000 genomes]
rs611943	0.93[EUR][1000 genomes]
rs612017	0.81[AMR][1000 genomes]
rs618454	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631033	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs631746	0.85[EUR][1000 genomes]
rs654224	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs655101	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs670498	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs674920	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs676007	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs679414	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687950	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs772159	0.82[EUR][1000 genomes]
rs772160	0.81[EUR][1000 genomes]
rs772161	0.82[EUR][1000 genomes]
rs772167	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs675239	ITPRIPL1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:55 , 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	chr2:97073200-97076600	Enhancers	Fetal Lung	lung
3	chr2:97073200-97076800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:97073200-97076800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:97073600-97076600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr2:97073600-97076600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:97073600-97076600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:97073600-97078400	Weak transcription	Esophagus	oesophagus
9	chr2:97073600-97078400	Weak transcription	Psoas Muscle	Psoas
10	chr2:97073800-97078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:97074000-97076800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:97074200-97076800	Enhancers	Spleen	Spleen
13	chr2:97074400-97076800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:97074400-97077400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:97074400-97078200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:97074400-97079400	Weak transcription	Gastric	stomach
17	chr2:97074600-97076600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:97074600-97077000	Enhancers	Brain Germinal Matrix	brain
19	chr2:97074800-97076600	Weak transcription	Pancreas	Pancrea
20	chr2:97074800-97078000	Weak transcription	K562	blood
21	chr2:97074800-97078200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:97074800-97078400	Weak transcription	Right Atrium	heart
23	chr2:97075200-97076600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr2:97075200-97078400	Weak transcription	Colonic Mucosa	Colon
25	chr2:97075200-97078800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:97075400-97078800	Weak transcription	Aorta	Aorta
27	chr2:97075600-97076600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:97075600-97078400	Weak transcription	Brain Anterior Caudate	brain
29	chr2:97075600-97079000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:97075600-97079400	Weak transcription	Fetal Kidney	kidney
31	chr2:97075800-97078400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:97075800-97078400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:97075800-97079000	Weak transcription	NH-A	brain
34	chr2:97076000-97078400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:97076000-97078400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:97076000-97078400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:97076000-97078400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:97076000-97078400	Weak transcription	HMEC	breast
39	chr2:97076000-97078600	Weak transcription	Brain Angular Gyrus	brain
40	chr2:97076000-97078600	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:97076000-97078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:97076000-97078600	Weak transcription	Brain Substantia Nigra	brain
43	chr2:97076000-97078600	Weak transcription	Fetal Thymus	thymus
44	chr2:97076000-97078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:97076000-97078800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:97076000-97078800	Weak transcription	Ovary	ovary
47	chr2:97076000-97079200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:97076200-97076600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr2:97076200-97076600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:97076200-97076600	Bivalent Enhancer	HepG2	liver

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