Variant report

Variant	rs1424954
Chromosome Location	chr2:148600794-148600795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:148599151-148601040	K562	blood:	n/a	n/a
2	SETDB1	chr2:148600430-148601443	U2OS	brain:	n/a	n/a
3	MAZ	chr2:148600775-148603017	IMR90	lung:	n/a	n/a
4	POLR2A	chr2:148599963-148602719	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:148567317..148569523-chr2:148600689..148602415,2	MCF-7	breast:
2	chr2:148600187..148601857-chr2:148665482..148668201,2	MCF-7	breast:
3	chr2:148445172..148447218-chr2:148598842..148601029,2	MCF-7	breast:
4	chr2:148589254..148592247-chr2:148597949..148601498,4	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ORC4-2	chr2:148600791-148601664	NONHSAT074859

No data

Variant related genes	Relation type
ACVR2A	TF binding region
ENSG00000229143	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1014064	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1015096	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs1020653	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1030317	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10460259	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10497024	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10803523	0.96[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1128919	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11884013	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11886876	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11888152	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11889608	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11900506	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs11901963	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11904758	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12053113	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12053401	0.96[CEU][hapmap];0.95[YRI][hapmap]
rs12104822	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12105745	0.96[YRI][hapmap]
rs1234416	0.92[YRI][hapmap]
rs12463798	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12464617	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12469015	0.88[EUR][1000 genomes]
rs12469504	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12469939	0.89[EUR][1000 genomes]
rs12472058	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12475399	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12479193	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12987286	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12989087	0.81[AFR][1000 genomes]
rs12989250	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12989596	0.94[EUR][1000 genomes]
rs12990262	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12990959	0.88[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12992412	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs12997065	0.89[EUR][1000 genomes]
rs12998729	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs13000597	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13004041	0.89[EUR][1000 genomes]
rs13004451	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13005423	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13006184	0.89[EUR][1000 genomes]
rs13008497	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs13012311	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13013743	0.98[EUR][1000 genomes]
rs13013867	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13014904	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs13014926	0.89[EUR][1000 genomes]
rs13016083	0.91[EUR][1000 genomes]
rs13016400	0.96[YRI][hapmap]
rs13017754	0.98[EUR][1000 genomes]
rs13019386	0.91[EUR][1000 genomes]
rs13019809	0.96[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13021605	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13021972	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13022319	0.88[EUR][1000 genomes]
rs13022962	0.96[CEU][hapmap];0.92[YRI][hapmap]
rs13025219	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13025589	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13025701	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13026220	0.98[EUR][1000 genomes]
rs13026650	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13027200	0.89[EUR][1000 genomes]
rs13027706	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13028348	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs13028411	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13029038	0.87[CEU][hapmap]
rs13031064	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13033589	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13033696	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13034494	0.97[EUR][1000 genomes]
rs13034561	0.90[EUR][1000 genomes]
rs13034793	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1345994	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1364658	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1364660	0.89[EUR][1000 genomes]
rs1424944	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1424946	0.90[EUR][1000 genomes]
rs1424949	0.89[EUR][1000 genomes]
rs1469210	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1531032	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1598207	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs16855486	0.90[EUR][1000 genomes]
rs1863152	0.88[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1863153	0.88[CEU][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1895693	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1975748	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs1991169	0.88[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2059422	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2113793	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2161983	0.96[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2161984	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2161985	0.88[EUR][1000 genomes]
rs2288190	0.84[CEU][hapmap];0.89[ASN][1000 genomes]
rs2303392	0.96[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2307394	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2382201	1.00[CEU][hapmap]
rs34005843	0.90[EUR][1000 genomes]
rs34539489	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35370215	0.88[EUR][1000 genomes]
rs3764955	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs3768687	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768689	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820716	0.96[YRI][hapmap]
rs3926960	0.82[EUR][1000 genomes]
rs4419186	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs4972272	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4972316	0.91[EUR][1000 genomes]
rs4972317	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4972318	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4972356	0.98[EUR][1000 genomes]
rs4972357	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57679331	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6430241	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6430242	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6711673	0.96[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6729465	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6729997	0.95[EUR][1000 genomes]
rs6734998	0.88[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6760703	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs723681	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7423878	0.86[AMR][1000 genomes]
rs7559714	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7559925	0.97[EUR][1000 genomes]
rs7594075	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7598361	1.00[CEU][hapmap]
rs7600869	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs897172	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs929939	0.92[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9679427	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs987122	0.92[AFR][1000 genomes];0.89[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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148599800-148600800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:148599800-148600800	Enhancers	Colon Smooth Muscle	Colon
3	chr2:148600000-148600800	Enhancers	Fetal Intestine Small	intestine
4	chr2:148600000-148600800	Enhancers	Fetal Kidney	kidney
5	chr2:148600200-148600800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:148600200-148600800	Enhancers	Rectal Smooth Muscle	rectum
7	chr2:148600400-148600800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:148600400-148600800	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:148600400-148600800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:148600400-148600800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:148600400-148600800	Enhancers	Brain Hippocampus Middle	brain
12	chr2:148600400-148600800	Enhancers	Fetal Stomach	stomach
13	chr2:148600400-148600800	Enhancers	Stomach Mucosa	stomach
14	chr2:148600400-148600800	Bivalent Enhancer	HepG2	liver
15	chr2:148600400-148601000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:148600400-148601000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
17	chr2:148600400-148601000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:148600400-148601200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:148600400-148601200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr2:148600400-148601600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:148600400-148604400	Active TSS	Stomach Smooth Muscle	stomach
22	chr2:148600400-148606200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:148600600-148600800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:148600600-148600800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:148600600-148600800	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr2:148600600-148600800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr2:148600600-148600800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
28	chr2:148600600-148600800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:148600600-148600800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:148600600-148600800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:148600600-148600800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:148600600-148600800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:148600600-148600800	Enhancers	Adipose Nuclei	Adipose
34	chr2:148600600-148600800	Enhancers	Brain Angular Gyrus	brain
35	chr2:148600600-148600800	Enhancers	Brain Germinal Matrix	brain
36	chr2:148600600-148600800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr2:148600600-148600800	Enhancers	Duodenum Mucosa	Duodenum
38	chr2:148600600-148600800	Enhancers	Fetal Brain Male	brain
39	chr2:148600600-148600800	Enhancers	Fetal Intestine Large	intestine
40	chr2:148600600-148600800	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr2:148600600-148600800	Enhancers	Fetal Lung	lung
42	chr2:148600600-148600800	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr2:148600600-148600800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr2:148600600-148600800	Enhancers	HUVEC	blood vessel
45	chr2:148600600-148600800	Enhancers	NH-A	brain
46	chr2:148600600-148600800	Enhancers	NHDF-Ad	bronchial
47	chr2:148600600-148600800	Active TSS	NHLF	lung
48	chr2:148600600-148601000	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr2:148600600-148601200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:148600600-148601200	Enhancers	Primary T helper cells fromperipheralblood	blood

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