Variant report

Variant	rs6546884
Chromosome Location	chr2:74237898-74237899
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74229526..74232576-chr2:74235829..74238698,3	K562	blood:
2	chr2:74233016..74235025-chr2:74236892..74238605,2	K562	blood:
3	chr2:74235618..74237940-chr2:74357623..74360543,2	MCF-7	breast:
4	chr2:74230663..74232784-chr2:74237198..74239379,3	K562	blood:
5	chr2:74237656..74239767-chr2:74475472..74477002,2	K562	blood:
6	chr2:74233183..74235025-chr2:74237105..74239040,2	K562	blood:
7	chr2:74005664..74007534-chr2:74236417..74239024,2	MCF-7	breast:
8	chr2:74233005..74244618-chr2:74246652..74253562,14	MCF-7	breast:
9	chr2:74236147..74237922-chr2:74424700..74426325,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000144048	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000187605	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10164943	0.85[EUR][1000 genomes]
rs10168249	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10168408	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10168410	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10179967	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10182376	0.86[ASN][1000 genomes]
rs10184542	0.82[ASN][1000 genomes]
rs10191539	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10200470	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11126424	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11884748	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11885172	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11886928	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11898903	0.84[EUR][1000 genomes]
rs12328927	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713803	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713804	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713805	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713806	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713808	0.84[EUR][1000 genomes]
rs12713809	0.85[EUR][1000 genomes]
rs12713810	0.82[EUR][1000 genomes]
rs12988533	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12995468	0.84[EUR][1000 genomes]
rs13005103	0.82[EUR][1000 genomes]
rs13006301	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13006407	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13011961	0.82[EUR][1000 genomes]
rs13013211	0.80[EUR][1000 genomes]
rs13014576	0.86[EUR][1000 genomes]
rs13016198	0.83[EUR][1000 genomes]
rs13021880	0.86[EUR][1000 genomes]
rs13027288	0.85[EUR][1000 genomes]
rs13027623	0.83[EUR][1000 genomes]
rs13030414	0.85[EUR][1000 genomes]
rs13387010	0.87[EUR][1000 genomes]
rs28450901	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34136450	0.80[EUR][1000 genomes]
rs35592918	0.85[EUR][1000 genomes]
rs35609589	0.86[EUR][1000 genomes]
rs3902790	0.85[EUR][1000 genomes]
rs4073048	0.85[EUR][1000 genomes]
rs4241260	0.87[EUR][1000 genomes]
rs4270374	0.93[EUR][1000 genomes]
rs4328662	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4331526	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4364046	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4371381	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4374402	0.85[EUR][1000 genomes]
rs4416242	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4422181	0.94[EUR][1000 genomes]
rs4574138	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4621184	0.86[EUR][1000 genomes]
rs4852326	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4853003	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4853005	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4853006	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4853007	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4853009	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60279245	0.84[EUR][1000 genomes]
rs6546885	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546886	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546887	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6706327	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6713313	0.89[EUR][1000 genomes]
rs6714186	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6717896	0.91[EUR][1000 genomes]
rs6741544	0.86[EUR][1000 genomes]
rs6743073	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745236	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6745576	0.85[EUR][1000 genomes]
rs6745792	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6754218	0.84[EUR][1000 genomes]
rs6755711	0.85[EUR][1000 genomes]
rs6756474	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71337722	0.84[EUR][1000 genomes]
rs7560668	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7584777	0.85[EUR][1000 genomes]
rs7587991	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7589915	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7592749	0.84[EUR][1000 genomes]
rs7593050	0.80[EUR][1000 genomes]
rs7597388	0.82[EUR][1000 genomes]
rs7601526	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7606491	0.84[EUR][1000 genomes]
rs9309478	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011177	chr2:74167343-74239905	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3584956	chr2:74197109-74317135	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv818048	chr2:74225434-74313080	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74230400-74246800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:74230600-74240000	Weak transcription	Aorta	Aorta
3	chr2:74230600-74248200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:74231200-74240000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:74231200-74246600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:74231600-74273800	Weak transcription	A549	lung
7	chr2:74232200-74238600	Strong transcription	Primary T cells from cord blood	blood
8	chr2:74233000-74247000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:74233400-74238000	Enhancers	Placenta	Placenta
10	chr2:74233400-74239200	Weak transcription	Hela-S3	cervix
11	chr2:74233400-74248600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:74234800-74247600	Weak transcription	HSMM	muscle
13	chr2:74235000-74238000	Enhancers	Small Intestine	intestine
14	chr2:74235000-74258400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:74235000-74259200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:74236000-74239800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:74236000-74246000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:74236200-74251200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:74236400-74238200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:74236400-74239000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:74236400-74251400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:74236400-74259400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:74236600-74239400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:74236600-74246600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:74236800-74238000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:74236800-74238800	Enhancers	Liver	Liver
27	chr2:74236800-74242000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:74236800-74245800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:74236800-74246800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:74236800-74247600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:74237000-74238000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr2:74237000-74241400	Weak transcription	Fetal Intestine Large	intestine
33	chr2:74237000-74246000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:74237200-74238000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:74237200-74238000	Enhancers	Fetal Lung	lung
36	chr2:74237200-74238400	Weak transcription	Primary B cells from cord blood	blood
37	chr2:74237200-74238800	Enhancers	Duodenum Mucosa	Duodenum
38	chr2:74237200-74239200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:74237200-74239400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:74237200-74243600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:74237400-74238000	Enhancers	Brain Hippocampus Middle	brain
42	chr2:74237400-74238600	Enhancers	Placenta Amnion	Placenta Amnion
43	chr2:74237400-74239600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:74237400-74246400	Weak transcription	Fetal Brain Female	brain
45	chr2:74237400-74246800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:74237400-74247000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:74237400-74247600	Weak transcription	HSMMtube	muscle
48	chr2:74237400-74247800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:74237400-74252800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr2:74237400-74259000	Weak transcription	NHLF	lung

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