Variant report

Variant	rs62169479
Chromosome Location	chr2:148606674-148606675
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:148606424..148608489-chr2:148610392..148613809,3	MCF-7	breast:
2	chr2:148600576..148604642-chr2:148604674..148611198,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121989	Chromatin interaction

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];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469211	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17218938	0.84[EUR][1000 genomes]
rs17225402	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17225423	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17225430	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17232078	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17691284	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17692648	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17741344	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17741978	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17742134	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17742246	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17742342	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17743157	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754541	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3820715	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62169472	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169473	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169474	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169475	0.86[ASN][1000 genomes]
rs62169477	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169478	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169480	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169481	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62169482	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62169483	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6747792	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs721344	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7595052	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7602296	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs929940	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs981814	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148604000-148612600	Weak transcription	Gastric	stomach
2	chr2:148604000-148620000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:148604600-148606800	Weak transcription	Fetal Stomach	stomach
4	chr2:148604600-148607200	Weak transcription	Psoas Muscle	Psoas
5	chr2:148604600-148607200	Weak transcription	Small Intestine	intestine
6	chr2:148604600-148607600	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:148604600-148607600	Weak transcription	Ovary	ovary
8	chr2:148604600-148607600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:148604600-148608400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:148604600-148608600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:148604600-148608800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:148604600-148610000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:148604600-148610000	Weak transcription	NHDF-Ad	bronchial
14	chr2:148604600-148612400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:148604600-148612400	Weak transcription	Left Ventricle	heart
16	chr2:148604600-148612400	Weak transcription	Right Ventricle	heart
17	chr2:148604600-148612600	Weak transcription	Pancreas	Pancrea
18	chr2:148604600-148614600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:148604600-148616400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:148604600-148617200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:148604600-148617600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:148604600-148617600	Weak transcription	HSMM	muscle
23	chr2:148604800-148607200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:148604800-148608400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:148604800-148609000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:148604800-148612800	Weak transcription	Right Atrium	heart
27	chr2:148605000-148608000	Enhancers	Fetal Brain Male	brain
28	chr2:148605200-148608600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:148605600-148607200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:148605600-148607200	Weak transcription	Stomach Mucosa	stomach
31	chr2:148605600-148612800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:148605600-148613200	Enhancers	HepG2	liver
33	chr2:148605600-148614600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:148605800-148607200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:148606000-148607200	Weak transcription	Fetal Brain Female	brain
36	chr2:148606000-148607800	Weak transcription	Liver	Liver
37	chr2:148606000-148612200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:148606000-148614200	Weak transcription	Brain Germinal Matrix	brain
39	chr2:148606000-148614600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:148606000-148620800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:148606000-148627600	Weak transcription	Brain Angular Gyrus	brain
42	chr2:148606200-148607200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:148606200-148607200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:148606200-148607200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:148606200-148607200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:148606200-148607200	Weak transcription	Colon Smooth Muscle	Colon
47	chr2:148606200-148607200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:148606200-148607400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:148606200-148607600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:148606200-148607600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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