Variant report

Variant	rs6712238
Chromosome Location	chr2:48339247-48339248
allele	A/C
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:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:48338567..48340069-chr2:48340476..48342562,2	K562	blood:
2	chr2:48337633..48340704-chr2:48540027..48544191,8	MCF-7	breast:
3	chr2:48339056..48340844-chr2:48670929..48673082,2	K562	blood:
4	chr2:48334851..48336463-chr2:48336834..48339382,2	K562	blood:
5	chr2:48337985..48339413-chr2:48647520..48648569,36	MCF-7	breast:
6	chr2:48337971..48339938-chr2:48647597..48648547,19	K562	blood:
7	chr2:48338775..48341219-chr2:48373264..48375327,2	K562	blood:
8	chr2:48337910..48340125-chr2:48569442..48571000,2	MCF-7	breast:
9	chr2:48333955..48336351-chr2:48337662..48339382,2	K562	blood:
10	chr2:48337578..48340434-chr2:48697185..48699414,2	MCF-7	breast:
11	chr2:48338863..48340413-chr2:48353804..48355488,2	MCF-7	breast:
12	chr14:77786713..77787244-chr2:48338531..48339263,2	HCT-116	colon:
13	chr2:48338352..48340381-chr2:48619344..48622319,2	K562	blood:
14	chr2:48337775..48340265-chr2:48597214..48600170,2	MCF-7	breast:
15	chr2:48336922..48340984-chr2:48645140..48651052,10	MCF-7	breast:
16	chr2:48336515..48341862-chr2:48539044..48543633,11	MCF-7	breast:
17	chr2:48337671..48340205-chr2:48664640..48667465,2	MCF-7	breast:
18	chr2:48337730..48339827-chr2:48662908..48664410,2	MCF-7	breast:
19	chr2:48337576..48339769-chr2:48655484..48657436,2	MCF-7	breast:
20	chr2:48131582..48133722-chr2:48336786..48340166,3	MCF-7	breast:
21	chr2:48337553..48343006-chr2:48644200..48649231,9	MCF-7	breast:
22	chr2:48337844..48339737-chr2:48667787..48670405,2	K562	blood:
23	chr2:48337541..48339290-chr2:48647557..48648526,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000233230	Chromatin interaction
ENSG00000170802	Chromatin interaction
ENSG00000100577	Chromatin interaction
ENSG00000009830	Chromatin interaction
ENSG00000162869	Chromatin interaction
ENSG00000138081	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10167776	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11125157	0.81[AMR][1000 genomes]
rs11125165	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11125166	0.81[ASN][1000 genomes]
rs1473611	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1483210	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1483215	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17324704	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1825320	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1878079	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1878081	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2128716	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2128719	0.83[ASN][1000 genomes]
rs2136456	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2348717	1.00[ASN][1000 genomes]
rs2348718	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28460586	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2882003	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4146603	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4952904	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4952905	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4953544	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4953546	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4953548	1.00[ASN][1000 genomes]
rs4953549	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953552	0.89[ASN][1000 genomes]
rs4953553	0.89[ASN][1000 genomes]
rs4953555	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953556	0.89[ASN][1000 genomes]
rs4953557	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58178746	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58525908	0.89[ASN][1000 genomes]
rs6545017	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6545019	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6545021	1.00[ASN][1000 genomes]
rs6545023	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6706664	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6718037	1.00[ASN][1000 genomes]
rs6722407	1.00[ASN][1000 genomes]
rs6723952	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750246	0.82[EUR][1000 genomes]
rs6759902	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7563749	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7570354	0.89[ASN][1000 genomes]
rs7589460	1.00[ASN][1000 genomes]
rs7605361	1.00[ASN][1000 genomes]
rs7605366	0.90[ASN][1000 genomes]
rs7609124	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900506	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs900510	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs900511	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs922902	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs922903	1.00[ASN][1000 genomes]
rs963133	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs963135	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9677729	0.89[ASN][1000 genomes]
rs968888	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs973894	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs990063	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs990549	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS 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
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription 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	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1000455	chr2:48202161-48362638	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv581773	chr2:48277490-48443109	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48337800-48339600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr2:48338000-48339600	Active TSS	Brain Germinal Matrix	brain
3	chr2:48338200-48339400	Active TSS	Aorta	Aorta
4	chr2:48338200-48339600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:48338200-48339600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:48338200-48339600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:48338200-48339600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr2:48338200-48339600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr2:48338200-48339600	Active TSS	Right Atrium	heart
10	chr2:48338200-48339600	Flanking Active TSS	Dnd41	blood
11	chr2:48338200-48339800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:48338400-48339400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:48338400-48339400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr2:48338400-48339400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:48338400-48339400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr2:48338400-48339400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr2:48338400-48339400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:48338400-48339400	Active TSS	Liver	Liver
19	chr2:48338400-48339400	Active TSS	Brain Hippocampus Middle	brain
20	chr2:48338400-48339400	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr2:48338400-48339400	Active TSS	Colonic Mucosa	Colon
22	chr2:48338400-48339400	Active TSS	Fetal Lung	lung
23	chr2:48338400-48339400	Active TSS	Small Intestine	intestine
24	chr2:48338400-48339400	Active TSS	Stomach Mucosa	stomach
25	chr2:48338400-48339600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:48338400-48339600	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr2:48338400-48339600	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr2:48338400-48339600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:48338400-48339600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr2:48338400-48339600	Active TSS	Muscle Satellite Cultured Cells	--
31	chr2:48338400-48339600	Active TSS	Brain Cingulate Gyrus	brain
32	chr2:48338400-48339600	Active TSS	Brain Substantia Nigra	brain
33	chr2:48338400-48339600	Active TSS	Colon Smooth Muscle	Colon
34	chr2:48338400-48339600	Active TSS	Fetal Brain Female	brain
35	chr2:48338400-48339600	Active TSS	Gastric	stomach
36	chr2:48338400-48339600	Active TSS	Left Ventricle	heart
37	chr2:48338400-48339600	Active TSS	Ovary	ovary
38	chr2:48338400-48339600	Active TSS	Psoas Muscle	Psoas
39	chr2:48338400-48339600	Active TSS	Rectal Smooth Muscle	rectum
40	chr2:48338400-48339600	Active TSS	Right Ventricle	heart
41	chr2:48338400-48339600	Active TSS	Stomach Smooth Muscle	stomach
42	chr2:48338400-48339600	Active TSS	HMEC	breast
43	chr2:48338400-48339600	Active TSS	HSMM	muscle
44	chr2:48338400-48339600	Active TSS	HSMMtube	muscle
45	chr2:48338400-48339600	Active TSS	K562	blood
46	chr2:48338400-48339600	Active TSS	NHDF-Ad	bronchial
47	chr2:48338400-48339600	Active TSS	NHLF	lung
48	chr2:48338400-48339800	Active TSS	Brain Anterior Caudate	brain
49	chr2:48338600-48339400	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr2:48338600-48339600	Flanking Active TSS	Primary B cells from cord blood	blood

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