Variant report

Variant	rs62154955
Chromosome Location	chr2:67626014-67626015
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:67625827-67626341	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:67623954-67626667	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:67623956-67626463	IMR90	lung:	n/a	n/a
4	GATA3	chr2:67625997-67626904	A549	lung:	n/a	n/a
5	BCL3	chr2:67625801-67626673	A549	lung:	n/a	n/a
6	POLR2A	chr2:67625891-67626428	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:67625062..67626828-chr2:67638770..67641070,2	K562	blood:
2	chr2:67625121..67629368-chr2:67632495..67635938,4	K562	blood:
3	chr2:67625330..67628840-chr2:67664328..67668176,3	MCF-7	breast:
4	chr2:67624773..67626495-chr2:67711958..67714968,3	MCF-7	breast:
5	chr2:67624297..67626969-chr2:67629233..67631299,3	K562	blood:
6	chr2:67624567..67629481-chr2:67631992..67635938,6	K562	blood:
7	chr2:67623626..67627299-chr2:67629860..67634637,7	MCF-7	breast:
8	chr2:67625560..67628357-chr2:68014133..68016829,2	K562	blood:

No data

Variant related genes	Relation type
ETAA1	TF binding region
ENSG00000143971	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10496153	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1063571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12185591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12185702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12988210	0.82[AMR][1000 genomes]
rs12991090	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12996359	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13000557	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13004747	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13004765	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13009070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13015319	0.82[AMR][1000 genomes]
rs13015349	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13016330	0.82[AMR][1000 genomes]
rs13017696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13018894	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13026513	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13030037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13030211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13034744	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13035051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13035754	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13036061	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1521051	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17544516	0.82[AMR][1000 genomes]
rs17544551	0.82[AMR][1000 genomes]
rs17545245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17545301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17545329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17603914	0.82[AMR][1000 genomes]
rs2171176	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34103917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34274370	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34281542	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34298852	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34418651	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34493710	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34547630	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34636997	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34737312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34920978	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34962808	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34997300	0.82[AMR][1000 genomes]
rs35002490	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35141978	0.82[AMR][1000 genomes]
rs35144434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35340993	0.82[AMR][1000 genomes]
rs35382600	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35503819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35570926	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35607813	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35610403	0.82[AMR][1000 genomes]
rs35686078	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35777125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36098430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4428006	0.88[EUR][1000 genomes]
rs62154898	0.82[AMR][1000 genomes]
rs62154948	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62154949	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62154950	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62154951	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62154952	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62154957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154958	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156688	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62156689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156693	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62156695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156696	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62156698	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62156699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156700	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156703	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156756	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62156757	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62156758	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62158290	0.82[AMR][1000 genomes]
rs71411986	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71411987	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71411988	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7585807	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008584	chr2:67168244-67703601	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535775	chr2:67168244-67703601	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv834249	chr2:67515471-67691605	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3335541	chr2:67577544-67773907	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67624000-67626200	Active TSS	Duodenum Mucosa	Duodenum
2	chr2:67624000-67626200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr2:67624000-67626200	Active TSS	K562	blood
4	chr2:67624000-67626400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:67624000-67626400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:67624000-67626600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr2:67624200-67626200	Active TSS	A549	lung
8	chr2:67624200-67626200	Active TSS	NHLF	lung
9	chr2:67625000-67629000	Flanking Active TSS	HUVEC	blood vessel
10	chr2:67625200-67626200	Flanking Active TSS	Dnd41	blood
11	chr2:67625200-67630600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:67625200-67633000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:67625200-67638200	Weak transcription	Left Ventricle	heart
14	chr2:67625400-67626200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:67625400-67626200	Weak transcription	Fetal Kidney	kidney
16	chr2:67625400-67626400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:67625400-67626400	Enhancers	Liver	Liver
18	chr2:67625400-67626400	Enhancers	NHDF-Ad	bronchial
19	chr2:67625400-67626800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:67625400-67627200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:67625400-67627200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:67625400-67627200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:67625400-67627200	Weak transcription	Fetal Intestine Large	intestine
24	chr2:67625400-67627200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:67625400-67627200	Weak transcription	Stomach Mucosa	stomach
26	chr2:67625400-67627800	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:67625400-67629200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr2:67625400-67629200	Weak transcription	Adipose Nuclei	Adipose
29	chr2:67625400-67629400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr2:67625400-67629600	Weak transcription	Primary B cells from cord blood	blood
31	chr2:67625400-67629600	Enhancers	Osteobl	bone
32	chr2:67625400-67630000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:67625400-67630400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:67625400-67630600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:67625400-67630600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:67625400-67631200	Weak transcription	Brain Anterior Caudate	brain
37	chr2:67625400-67631200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:67625400-67633200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:67625400-67633800	Weak transcription	Brain Substantia Nigra	brain
40	chr2:67625400-67634400	Weak transcription	Ovary	ovary
41	chr2:67625400-67636000	Weak transcription	Brain Germinal Matrix	brain
42	chr2:67625400-67639400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:67625400-67639400	Weak transcription	Psoas Muscle	Psoas
44	chr2:67625400-67639800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:67625400-67640000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:67625400-67640200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:67625400-67640400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr2:67625400-67641200	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:67625400-67641400	Weak transcription	HSMMtube	muscle
50	chr2:67625400-67643000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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