Variant report

Variant	rs778338
Chromosome Location	chr2:233740227-233740228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:233740065-233741988	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:233739914-233740702	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:233739984-233740692	A549	lung:	n/a	n/a
4	RAD21	chr2:233740153-233740727	SK-N-SH	brain:	n/a	n/a
5	RAD21	chr2:233740184-233740746	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr2:233740119-233740687	HepG2	liver:	n/a	n/a
7	HEY1	chr2:233740209-233740740	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:233740143-233742085	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr2:233735463-233740850	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:233737594-233750472	HepG2	liver:	n/a	n/a
11	CTCF	chr2:233740098-233740864	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr2:233739950-233740745	HepG2	liver:	n/a	n/a
13	HEY1	chr2:233740002-233740801	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:233733606..233736578-chr2:233738541..233742093,3	K562	blood:
2	chr2:233739500..233741658-chr2:234118418..234121019,2	MCF-7	breast:
3	chr2:233738643..233740986-chr2:234158854..234161597,2	MCF-7	breast:
4	chr2:233739591..233745527-chr2:233747956..233752237,8	MCF-7	breast:
5	chr2:233739669..233741368-chr2:233754744..233756796,2	MCF-7	breast:
6	chr2:233739634..233741752-chr2:234762062..234763820,2	MCF-7	breast:
7	chr2:233733606..233736774-chr2:233738541..233741120,3	K562	blood:

No data

Variant related genes	Relation type
C2orf82	TF binding region
ENSG00000085978	Chromatin interaction
ENSG00000123485	Chromatin interaction
ENSG00000066248	Chromatin interaction
ENSG00000182600	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1022330	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10933411	0.96[ASN][1000 genomes]
rs10933412	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11555646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs11676216	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[ASN][1000 genomes]
rs11679079	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs12474040	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12694917	0.96[ASN][1000 genomes]
rs12990821	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs13003675	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs13004406	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs13011298	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13013142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1446308	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1446310	0.85[ASN][1000 genomes]
rs1446311	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs1801251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1867778	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1947105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2012221	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2044449	0.98[ASN][1000 genomes]
rs2100053	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2197563	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2250654	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2250665	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305137	0.96[ASN][1000 genomes]
rs2305141	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2592102	0.98[ASN][1000 genomes]
rs2592113	0.85[ASN][1000 genomes]
rs2592115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592126	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2674839	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs2675957	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2675966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675971	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2675973	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2675974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs283466	0.85[ASN][1000 genomes]
rs283468	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs283469	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs283471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs283474	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs283475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs283476	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs283486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs3816334	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3817311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4973053	0.85[ASN][1000 genomes]
rs4973054	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4973055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4973056	0.95[ASN][1000 genomes]
rs4973560	0.83[ASN][1000 genomes]
rs4973561	0.85[ASN][1000 genomes]
rs6437074	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6704768	0.81[JPT][hapmap]
rs6714245	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6717841	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6719061	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs6738386	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6745879	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6746294	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6747645	0.85[JPT][hapmap]
rs6748027	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs709933	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709938	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737028	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7558609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs7568385	0.81[ASN][1000 genomes]
rs7573208	0.87[ASN][1000 genomes]
rs7587309	0.95[ASN][1000 genomes]
rs7589201	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7606090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs778166	0.80[ASN][1000 genomes]
rs778339	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778368	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs809639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs812383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9653383	0.84[ASN][1000 genomes]
rs991873	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv984452	chr2:233725452-233762965	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv999116	chr2:233733352-233759864	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1007029	chr2:233733352-233760519	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv536179	chr2:233735380-233757170	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3395649	chr2:233739733-233742581	Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs778338	C2orf82	cis	Temporal Cortex	GTEx
rs778338	C2orf82	cis	Skin Sun Exposed Lower leg	GTEx
rs778338	C2orf82	cis	Frontal Cortex	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233723000-233740400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:233726000-233740400	Weak transcription	HMEC	breast
3	chr2:233726400-233740400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:233726400-233740800	Weak transcription	HSMM	muscle
5	chr2:233726600-233740400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:233726600-233740400	Weak transcription	Lung	lung
7	chr2:233726600-233740400	Weak transcription	NHEK	skin
8	chr2:233726800-233755600	Weak transcription	HSMMtube	muscle
9	chr2:233734400-233740400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr2:233738200-233740400	Enhancers	Liver	Liver
11	chr2:233738600-233740600	Enhancers	Spleen	Spleen
12	chr2:233738800-233741000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:233739400-233740400	Weak transcription	Esophagus	oesophagus
14	chr2:233739400-233740600	Enhancers	Gastric	stomach
15	chr2:233739400-233740600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
16	chr2:233739400-233740600	Bivalent Enhancer	Stomach Mucosa	stomach
17	chr2:233739800-233740600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr2:233740000-233740400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:233740000-233740400	Weak transcription	Ovary	ovary
20	chr2:233740000-233740400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr2:233740000-233740400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
22	chr2:233740000-233740400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
23	chr2:233740000-233740600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:233740000-233740600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:233740000-233740600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
26	chr2:233740000-233740600	Flanking Active TSS	Fetal Intestine Small	intestine
27	chr2:233740000-233740600	Enhancers	Pancreas	Pancrea
28	chr2:233740000-233740600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr2:233740000-233740600	Flanking Active TSS	HepG2	liver
30	chr2:233740000-233740800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:233740000-233740800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr2:233740000-233741000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
33	chr2:233740000-233741000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:233740000-233742000	Bivalent Enhancer	Placenta	Placenta
35	chr2:233740200-233740400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:233740200-233740400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr2:233740200-233740400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr2:233740200-233740400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:233740200-233740400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:233740200-233740400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
41	chr2:233740200-233740400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:233740200-233740400	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr2:233740200-233740400	Flanking Active TSS	Colonic Mucosa	Colon
44	chr2:233740200-233740400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr2:233740200-233740400	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr2:233740200-233740400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr2:233740200-233740400	Enhancers	Psoas Muscle	Psoas
48	chr2:233740200-233740400	Bivalent Enhancer	Right Ventricle	heart
49	chr2:233740200-233740400	Flanking Active TSS	Hela-S3	cervix
50	chr2:233740200-233740600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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