Variant report

Variant	rs13034494
Chromosome Location	chr2:148615530-148615531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:148599031..148600607-chr2:148614779..148616872,2	MCF-7	breast:
2	chr2:148601772..148604478-chr2:148614345..148616286,2	MCF-7	breast:
3	chr2:148601400..148602915-chr2:148613570..148615600,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121989	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1014064	0.98[EUR][1000 genomes]
rs1020653	0.85[EUR][1000 genomes]
rs1030317	0.90[EUR][1000 genomes]
rs10460259	0.91[EUR][1000 genomes]
rs10497024	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10803523	0.98[EUR][1000 genomes]
rs1128919	0.97[EUR][1000 genomes]
rs11884013	0.87[EUR][1000 genomes]
rs11888152	0.90[EUR][1000 genomes]
rs11889608	0.96[EUR][1000 genomes]
rs11901963	0.90[EUR][1000 genomes]
rs11904758	0.99[EUR][1000 genomes]
rs12053113	0.94[EUR][1000 genomes]
rs12104822	0.88[EUR][1000 genomes]
rs12463798	0.90[EUR][1000 genomes]
rs12464617	0.96[EUR][1000 genomes]
rs12469015	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12469504	0.87[EUR][1000 genomes]
rs12469939	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12472058	0.87[EUR][1000 genomes]
rs12475399	0.87[EUR][1000 genomes]
rs12479193	0.87[EUR][1000 genomes]
rs12987286	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12989596	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12990262	0.87[EUR][1000 genomes]
rs12990959	0.89[EUR][1000 genomes]
rs12997065	0.87[EUR][1000 genomes]
rs12998729	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13000597	0.98[EUR][1000 genomes]
rs13004041	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13004451	0.94[EUR][1000 genomes]
rs13005423	0.85[EUR][1000 genomes]
rs13006184	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13008497	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13012311	0.90[EUR][1000 genomes]
rs13013743	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13013867	0.96[EUR][1000 genomes]
rs13014904	0.88[EUR][1000 genomes]
rs13014926	0.86[EUR][1000 genomes]
rs13016083	0.90[EUR][1000 genomes]
rs13017754	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13019386	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13019809	0.95[EUR][1000 genomes]
rs13021972	0.82[EUR][1000 genomes]
rs13022319	0.86[EUR][1000 genomes]
rs13025219	0.94[EUR][1000 genomes]
rs13025589	0.96[EUR][1000 genomes]
rs13025701	0.86[EUR][1000 genomes]
rs13026220	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13026650	0.97[EUR][1000 genomes]
rs13027200	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13027706	0.91[EUR][1000 genomes]
rs13028411	0.97[EUR][1000 genomes]
rs13031064	0.91[EUR][1000 genomes]
rs13033589	0.90[EUR][1000 genomes]
rs13033696	0.99[EUR][1000 genomes]
rs13034561	0.89[EUR][1000 genomes]
rs13034793	0.90[EUR][1000 genomes]
rs1345994	0.93[EUR][1000 genomes]
rs1364658	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364660	0.88[EUR][1000 genomes]
rs1424944	0.96[EUR][1000 genomes]
rs1424946	0.89[EUR][1000 genomes]
rs1424949	0.86[EUR][1000 genomes]
rs1424954	0.97[EUR][1000 genomes]
rs1469210	0.98[EUR][1000 genomes]
rs1531032	0.91[EUR][1000 genomes]
rs16855486	0.89[EUR][1000 genomes]
rs1863152	0.87[EUR][1000 genomes]
rs1863153	0.87[EUR][1000 genomes]
rs1895693	0.98[EUR][1000 genomes]
rs1991169	0.87[EUR][1000 genomes]
rs2059422	0.91[EUR][1000 genomes]
rs2161983	0.97[EUR][1000 genomes]
rs2161985	0.88[EUR][1000 genomes]
rs2303392	0.94[EUR][1000 genomes]
rs2307394	0.91[EUR][1000 genomes]
rs34005843	0.89[EUR][1000 genomes]
rs34539489	0.91[EUR][1000 genomes]
rs35370215	0.87[EUR][1000 genomes]
rs3764955	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768687	0.97[EUR][1000 genomes]
rs3768689	0.97[EUR][1000 genomes]
rs4972272	0.87[EUR][1000 genomes]
rs4972316	0.88[EUR][1000 genomes]
rs4972317	0.90[EUR][1000 genomes]
rs4972318	0.90[EUR][1000 genomes]
rs4972356	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972357	0.94[EUR][1000 genomes]
rs57679331	0.91[EUR][1000 genomes]
rs6430241	0.86[EUR][1000 genomes]
rs6430242	0.86[EUR][1000 genomes]
rs6711673	0.98[EUR][1000 genomes]
rs6729465	0.91[EUR][1000 genomes]
rs6729997	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6734998	0.87[EUR][1000 genomes]
rs6760703	0.93[EUR][1000 genomes]
rs723681	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7559714	0.99[EUR][1000 genomes]
rs7559925	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7594075	0.91[EUR][1000 genomes]
rs7600869	0.86[EUR][1000 genomes]
rs929939	0.98[EUR][1000 genomes]
rs9679427	0.86[EUR][1000 genomes]
rs987122	0.87[EUR][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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148604000-148620000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:148604600-148616400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:148604600-148617200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:148604600-148617600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:148604600-148617600	Weak transcription	HSMM	muscle
6	chr2:148606000-148620800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:148606000-148627600	Weak transcription	Brain Angular Gyrus	brain
8	chr2:148606200-148620800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:148607400-148617400	Weak transcription	Fetal Brain Female	brain
10	chr2:148607800-148615600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:148608600-148616800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:148608800-148617400	Weak transcription	HSMMtube	muscle
13	chr2:148609000-148617000	Weak transcription	Adipose Nuclei	Adipose
14	chr2:148609400-148616000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:148609400-148619600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:148609400-148620800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:148610400-148616200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:148612200-148615600	Weak transcription	Ovary	ovary
19	chr2:148613000-148615600	Weak transcription	Psoas Muscle	Psoas
20	chr2:148613000-148615800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:148613000-148616800	Weak transcription	Left Ventricle	heart
22	chr2:148613000-148617600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:148613000-148617600	Weak transcription	Gastric	stomach
24	chr2:148613000-148627400	Weak transcription	Pancreas	Pancrea
25	chr2:148613000-148640800	Weak transcription	Lung	lung
26	chr2:148613200-148616000	Weak transcription	Fetal Heart	heart
27	chr2:148613200-148616000	Weak transcription	HepG2	liver
28	chr2:148613200-148616800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:148613200-148619800	Weak transcription	Fetal Intestine Large	intestine
30	chr2:148613200-148625600	Weak transcription	Right Atrium	heart
31	chr2:148613200-148631400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:148613800-148615600	Weak transcription	Stomach Mucosa	stomach
33	chr2:148613800-148616800	Weak transcription	Liver	Liver
34	chr2:148613800-148617000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:148613800-148617600	Weak transcription	Right Ventricle	heart
36	chr2:148614000-148616000	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:148614000-148617200	Weak transcription	Fetal Brain Male	brain
38	chr2:148614200-148617000	Enhancers	Brain Germinal Matrix	brain
39	chr2:148614400-148620400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:148614600-148618800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:148614600-148621400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr2:148614800-148616400	Enhancers	Brain Hippocampus Middle	brain
43	chr2:148614800-148618600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr2:148615000-148616200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:148615000-148617000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:148615200-148619200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:148615400-148616200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:148615400-148616200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:148615400-148623200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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