Variant report

Variant	rs61824005
Chromosome Location	chr1:223965331-223965332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223962795..223965332-chr1:223971942..223974529,2	MCF-7	breast:
2	chr1:223963678..223965636-chr1:223966961..223968490,2	MCF-7	breast:
3	chr1:223893121..223894903-chr1:223963309..223965423,3	MCF-7	breast:
4	chr1:223964914..223967856-chr1:224032399..224034591,2	K562	blood:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10159015	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10465524	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10503144	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10915702	0.82[EUR][1000 genomes]
rs10915707	0.85[EUR][1000 genomes]
rs10915715	0.85[EUR][1000 genomes]
rs1153957	0.80[EUR][1000 genomes]
rs1153958	0.81[EUR][1000 genomes]
rs1153965	0.94[EUR][1000 genomes]
rs12022914	0.81[ASN][1000 genomes]
rs12022920	0.81[ASN][1000 genomes]
rs12024059	0.81[ASN][1000 genomes]
rs12026548	0.85[ASN][1000 genomes]
rs12028843	0.81[ASN][1000 genomes]
rs12031859	0.81[ASN][1000 genomes]
rs12038665	0.81[ASN][1000 genomes]
rs12043790	0.85[ASN][1000 genomes]
rs12044358	0.85[ASN][1000 genomes]
rs12046297	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12059128	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12059770	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12060361	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12066704	0.82[EUR][1000 genomes]
rs12066829	0.82[EUR][1000 genomes]
rs12066831	0.82[EUR][1000 genomes]
rs12069561	0.85[EUR][1000 genomes]
rs12070057	0.82[EUR][1000 genomes]
rs12080250	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12088254	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091841	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1222134	0.85[EUR][1000 genomes]
rs1222138	0.81[EUR][1000 genomes]
rs1222140	0.82[EUR][1000 genomes]
rs1222141	0.82[EUR][1000 genomes]
rs12562109	0.85[EUR][1000 genomes]
rs12563291	0.87[EUR][1000 genomes]
rs12563477	0.96[EUR][1000 genomes]
rs12563637	0.84[EUR][1000 genomes]
rs12563713	0.89[EUR][1000 genomes]
rs12565967	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12566817	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1542507	0.81[ASN][1000 genomes]
rs16842162	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16842229	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16842257	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16842259	0.81[ASN][1000 genomes]
rs16842326	0.88[EUR][1000 genomes]
rs17597	0.87[EUR][1000 genomes]
rs17598	0.85[EUR][1000 genomes]
rs17600	0.85[EUR][1000 genomes]
rs28370069	0.86[EUR][1000 genomes]
rs28370073	0.93[EUR][1000 genomes]
rs28370074	0.93[EUR][1000 genomes]
rs28370088	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28370159	0.91[EUR][1000 genomes]
rs28370160	0.83[ASN][1000 genomes]
rs28370166	0.85[ASN][1000 genomes]
rs28370170	0.96[EUR][1000 genomes]
rs28370174	0.85[ASN][1000 genomes]
rs28370177	0.85[ASN][1000 genomes]
rs28370178	0.85[ASN][1000 genomes]
rs34683843	0.99[EUR][1000 genomes]
rs36032024	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3738373	0.85[EUR][1000 genomes]
rs3738374	0.85[EUR][1000 genomes]
rs3738375	0.85[EUR][1000 genomes]
rs3767710	0.85[ASN][1000 genomes]
rs3767716	0.83[EUR][1000 genomes]
rs3767717	0.85[EUR][1000 genomes]
rs3767718	0.85[EUR][1000 genomes]
rs3820474	0.81[ASN][1000 genomes]
rs3885657	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59275322	0.82[EUR][1000 genomes]
rs61437308	0.81[ASN][1000 genomes]
rs61823580	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61823581	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61823583	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61823585	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61823587	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61823591	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61824003	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61824008	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6604724	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6604727	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6604728	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6604729	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6604730	0.88[EUR][1000 genomes]
rs6658954	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6665485	0.83[EUR][1000 genomes]
rs6674541	0.82[EUR][1000 genomes]
rs6674846	0.82[EUR][1000 genomes]
rs6678365	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6682964	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6685557	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6691315	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6694960	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6696053	0.81[EUR][1000 genomes]
rs6700366	0.94[EUR][1000 genomes]
rs7331	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs747811	0.85[ASN][1000 genomes]
rs751609	0.82[EUR][1000 genomes]
rs7528455	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7530328	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7533551	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7535882	0.88[EUR][1000 genomes]
rs7552702	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555226	0.82[EUR][1000 genomes]
rs898876	0.82[EUR][1000 genomes]
rs898877	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223956600-223967000	Strong transcription	Lung	lung
2	chr1:223956600-223967200	Strong transcription	Colonic Mucosa	Colon
3	chr1:223956600-223968400	Strong transcription	Fetal Brain Female	brain
4	chr1:223956600-223969000	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:223956600-223969000	Strong transcription	Fetal Stomach	stomach
6	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:223956800-223969000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:223956800-223969200	Strong transcription	Placenta	Placenta
10	chr1:223956800-223974200	Strong transcription	Primary T cells from cord blood	blood
11	chr1:223956800-223974200	Strong transcription	Liver	Liver
12	chr1:223957000-223983400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:223957200-223968000	Strong transcription	Brain Germinal Matrix	brain
14	chr1:223957200-223968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:223957200-223972800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:223959600-223966600	Weak transcription	Fetal Brain Male	brain
17	chr1:223959600-223969000	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:223959800-223977600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:223960000-223968600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:223960000-223969000	Strong transcription	Fetal Kidney	kidney
21	chr1:223960000-223972200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:223960200-223970000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:223960200-223971800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr1:223960200-223998600	Strong transcription	Fetal Thymus	thymus
25	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:223960400-223968800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:223960600-223967200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:223960600-223986800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:223960600-223995200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:223960600-224001400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:223960800-223967400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr1:223960800-223967600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:223960800-223968600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:223960800-223995400	Weak transcription	GM12878-XiMat	blood
35	chr1:223961000-223966200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:223961200-223966600	Strong transcription	Brain Hippocampus Middle	brain
37	chr1:223961200-223967000	Strong transcription	Brain Substantia Nigra	brain
38	chr1:223961200-223968400	Strong transcription	Fetal Lung	lung
39	chr1:223961400-223966400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:223961400-223968800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr1:223961400-223969000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:223961600-223968000	Strong transcription	Brain Anterior Caudate	brain
43	chr1:223961800-223967000	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr1:223961800-223969000	Strong transcription	Rectal Smooth Muscle	rectum
45	chr1:223961800-223972200	Strong transcription	Dnd41	blood
46	chr1:223961800-223977200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:223961800-224004400	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:223962000-223975000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:223962600-223970600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:223962600-223983600	Weak transcription	Psoas Muscle	Psoas

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