Variant report

Variant	rs2278652
Chromosome Location	chr1:211751025-211751026
allele	C/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:211750915..211755112-chr1:211826013..211829699,5	K562	blood:
2	chr1:211750437..211753125-chr1:211823737..211827672,4	MCF-7	breast:
3	chr1:211749200..211754595-chr1:211816014..211824648,8	K562	blood:
4	chr1:211750781..211751639-chr1:211798078..211798633,2	MCF-7	breast:
5	chr1:211750433..211752019-chr1:211835257..211837969,2	K562	blood:
6	chr1:211750650..211751428-chr1:211803176..211803710,2	MCF-7	breast:
7	chr1:211429991..211432106-chr1:211750411..211752434,2	MCF-7	breast:
8	chr1:211750816..211751334-chr1:211828394..211828945,2	MCF-7	breast:
9	chr1:211750794..211754252-chr1:211815868..211819773,4	MCF-7	breast:
10	chr1:211750060..211753695-chr1:211824093..211827463,4	MCF-7	breast:
11	chr1:211750683..211751727-chr1:211803429..211804168,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228792	Chromatin interaction
ENSG00000117625	Chromatin interaction
ENSG00000222080	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11119772	0.92[JPT][hapmap]
rs11553543	0.92[AFR][1000 genomes]
rs12091351	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12562288	1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs17017739	0.91[JPT][hapmap]
rs17017761	0.84[AFR][1000 genomes]
rs17017782	0.92[JPT][hapmap]
rs17838268	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738198	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60420078	0.80[ASN][1000 genomes]
rs61336072	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61632665	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6676167	0.81[ASN][1000 genomes]
rs73073202	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73075103	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73075106	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73075108	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73075115	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73075131	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7515127	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7519865	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7530862	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7531277	0.85[AFR][1000 genomes]
rs7543376	0.92[JPT][hapmap]

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	nsv832514	chr1:211630247-211794963	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv1796467	chr1:211726975-211769893	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv1840920	chr1:211726975-211769893	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv1836726	chr1:211736470-211752981	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv549125	chr1:211750362-211753094	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
6	nsv826542	chr1:211750561-211752995	Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	esv3374509	chr1:211750979-211753977	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2278652	ANGEL2	cis	cerebellum	SCAN
rs2278652	C1orf97	cis	parietal	SCAN
rs2278652	TRAF3IP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211748600-211753200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:211748800-211751400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:211749000-211753400	Active TSS	Aorta	Aorta
4	chr1:211749000-211753400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:211749400-211751400	Active TSS	Stomach Smooth Muscle	stomach
6	chr1:211749400-211753200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:211749400-211753200	Active TSS	Fetal Stomach	stomach
8	chr1:211749400-211753200	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr1:211749400-211753400	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr1:211749600-211753000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:211749600-211753000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:211749600-211753000	Active TSS	GM12878-XiMat	blood
13	chr1:211749600-211753000	Active TSS	HMEC	breast
14	chr1:211749600-211753000	Active TSS	HSMMtube	muscle
15	chr1:211749600-211753000	Active TSS	NH-A	brain
16	chr1:211749600-211753000	Active TSS	NHLF	lung
17	chr1:211749600-211753200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:211749600-211753200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:211749600-211753200	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr1:211749600-211753200	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:211749600-211753200	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr1:211749600-211753200	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:211749600-211753200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:211749600-211753200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:211749600-211753200	Active TSS	Duodenum Mucosa	Duodenum
26	chr1:211749600-211753200	Active TSS	Fetal Intestine Large	intestine
27	chr1:211749600-211753200	Active TSS	Fetal Kidney	kidney
28	chr1:211749600-211753200	Active TSS	Rectal Smooth Muscle	rectum
29	chr1:211749600-211753200	Active TSS	A549	lung
30	chr1:211749600-211753200	Active TSS	Hela-S3	cervix
31	chr1:211749600-211753200	Active TSS	K562	blood
32	chr1:211749600-211753200	Active TSS	NHDF-Ad	bronchial
33	chr1:211749600-211753800	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr1:211749800-211751200	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr1:211749800-211751400	Active TSS	Colonic Mucosa	Colon
36	chr1:211749800-211751600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:211749800-211752000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:211749800-211753000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:211749800-211753000	Active TSS	Fetal Muscle Leg	muscle
40	chr1:211749800-211753200	Active TSS	NHEK	skin
41	chr1:211749800-211753400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:211749800-211753400	Active TSS	Fetal Muscle Trunk	muscle
43	chr1:211750000-211752600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr1:211750000-211753000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr1:211750000-211753000	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr1:211750000-211753000	Active TSS	Osteobl	bone
47	chr1:211750000-211753200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:211750000-211753200	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr1:211750000-211753200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:211750000-211753200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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