Variant report

Variant	rs17741978
Chromosome Location	chr2:148617380-148617381
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1424941	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469211	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17218938	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17225402	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17225423	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17225430	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17232078	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17691284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17692648	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17741344	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17742134	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17742246	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17742342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17743157	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754541	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3820715	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62169472	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169473	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169474	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169475	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62169477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169478	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169479	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62169480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs721344	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs730356	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7560502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595052	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7602296	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs929940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981814	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875275	chr2:148166428-148711242	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148604000-148620000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:148604600-148617600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:148604600-148617600	Weak transcription	HSMM	muscle
4	chr2:148606000-148620800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:148606000-148627600	Weak transcription	Brain Angular Gyrus	brain
6	chr2:148606200-148620800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:148607400-148617400	Weak transcription	Fetal Brain Female	brain
8	chr2:148608800-148617400	Weak transcription	HSMMtube	muscle
9	chr2:148609400-148619600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:148609400-148620800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:148613000-148617600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:148613000-148617600	Weak transcription	Gastric	stomach
13	chr2:148613000-148627400	Weak transcription	Pancreas	Pancrea
14	chr2:148613000-148640800	Weak transcription	Lung	lung
15	chr2:148613200-148619800	Weak transcription	Fetal Intestine Large	intestine
16	chr2:148613200-148625600	Weak transcription	Right Atrium	heart
17	chr2:148613200-148631400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:148613800-148617600	Weak transcription	Right Ventricle	heart
19	chr2:148614400-148620400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:148614600-148618800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:148614600-148621400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr2:148614800-148618600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr2:148615200-148619200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:148615400-148623200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:148615600-148617800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:148615600-148618000	Enhancers	Psoas Muscle	Psoas
27	chr2:148615600-148618400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:148615800-148618000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:148615800-148618400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:148615800-148618800	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr2:148615800-148621000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr2:148615800-148626200	Weak transcription	Ovary	ovary
33	chr2:148616000-148617400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:148616000-148618400	Enhancers	Fetal Heart	heart
35	chr2:148616200-148617600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:148616200-148617800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr2:148616200-148618400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:148616200-148618800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr2:148616200-148619600	Weak transcription	Stomach Mucosa	stomach
40	chr2:148616200-148621000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:148616400-148617400	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:148616400-148619800	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr2:148616600-148617800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:148616600-148620400	Weak transcription	Fetal Intestine Small	intestine
45	chr2:148616800-148617400	Enhancers	Liver	Liver
46	chr2:148616800-148617800	Enhancers	Placenta Amnion	Placenta Amnion
47	chr2:148616800-148618000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:148616800-148618000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:148616800-148618400	Enhancers	H1 Cell Line	embryonic stem cell
50	chr2:148616800-148618400	Enhancers	Skeletal Muscle Female	skeletal muscle

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