Variant report

Variant	rs2139403
Chromosome Location	chr2:101178351-101178352
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr2:101178201-101180511	K562	blood:	n/a	chr2:101179689-101179698 chr2:101180362-101180373
2	MAZ	chr2:101178134-101180445	IMR90	lung:	n/a	chr2:101178474-101178489
3	POLR2A	chr2:101178334-101178715	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr2:101178225-101180195	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr2:101178255-101180576	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:101178202-101180048	GM12878	blood:	n/a	n/a
7	RCOR1	chr2:101177752-101180458	IMR90	lung:	n/a	n/a
8	POLR2A	chr2:101178297-101180233	K562	blood:	n/a	n/a
9	CCNT2	chr2:101178239-101178802	K562	blood:	n/a	n/a
10	POLR2A	chr2:101178337-101180558	GM12892	blood:	n/a	n/a
11	RPC155	chr2:101178321-101179291	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr2:101178312-101178714	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr2:101178278-101180076	Raji	blood:	n/a	n/a
14	POLR2A	chr2:101178202-101180334	GM12891	blood:	n/a	n/a
15	POLR2A	chr2:101178339-101180288	K562	blood:	n/a	n/a
16	POLR2A	chr2:101178240-101178736	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr2:101178209-101178379	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr2:101178271-101179997	GM12878	blood:	n/a	n/a
19	MAX	chr2:101178341-101178641	H1-hESC	embryonic stem cell:	n/a	chr2:101178474-101178489

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:101176864..101179772-chr2:101619065..101621695,2	MCF-7	breast:
2	chr2:101033038..101035627-chr2:101178228..101182939,5	K562	blood:
3	chr2:101177750..101180702-chr2:101616968..101620230,4	MCF-7	breast:
4	chr2:101177817..101179680-chr2:101183661..101186374,4	K562	blood:
5	chr2:101177993..101180966-chr2:101192692..101194735,2	K562	blood:
6	chr2:101177732..101180772-chr2:101616573..101620250,3	K562	blood:
7	chr2:101176287..101178582-chr2:101217009..101219585,2	K562	blood:

No data

Variant related genes	Relation type
PDCL3	TF binding region
ENSG00000071082	Chromatin interaction
ENSG00000265839	Chromatin interaction
ENSG00000223947	Chromatin interaction
ENSG00000238328	Chromatin interaction
ENSG00000115526	Chromatin interaction
ENSG00000115539	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13387441	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13422218	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2946589	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2946593	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2970990	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4850933	0.81[MEX][hapmap]
rs6716842	0.81[MEX][hapmap]
rs7557273	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs962555	0.82[CEU][hapmap]
rs962556	0.81[MEX][hapmap]
rs964559	0.89[CEU][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv834312	chr2:101044438-101238166	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101171800-101178400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:101174600-101178400	Weak transcription	HSMMtube	muscle
3	chr2:101176800-101178400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:101176800-101178400	Enhancers	HepG2	liver
5	chr2:101177000-101178400	Enhancers	Primary T cells from cord blood	blood
6	chr2:101177000-101178400	Enhancers	GM12878-XiMat	blood
7	chr2:101177200-101178400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:101177200-101178400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr2:101177200-101178400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:101177200-101178600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:101177600-101178400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr2:101177600-101178400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:101177600-101178600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:101177800-101178400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:101177800-101178400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr2:101177800-101178400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr2:101177800-101178400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr2:101177800-101178400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:101177800-101178400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:101177800-101178400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr2:101177800-101178400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr2:101177800-101178400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:101177800-101178400	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:101177800-101178400	Enhancers	Brain Hippocampus Middle	brain
25	chr2:101177800-101178400	Enhancers	Duodenum Mucosa	Duodenum
26	chr2:101177800-101178600	Enhancers	Primary B cells from cord blood	blood
27	chr2:101177800-101178600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr2:101177800-101178600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:101177800-101178600	Enhancers	Fetal Thymus	thymus
30	chr2:101178000-101178400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr2:101178000-101178400	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr2:101178000-101178400	Enhancers	Brain Substantia Nigra	brain
33	chr2:101178000-101178400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr2:101178000-101178600	Enhancers	Primary B cells from peripheral blood	blood
35	chr2:101178200-101178400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:101178200-101178400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:101178200-101178400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr2:101178200-101178400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:101178200-101178400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:101178200-101178400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:101178200-101178400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:101178200-101178400	Enhancers	Brain Angular Gyrus	brain
43	chr2:101178200-101178400	Enhancers	Brain Anterior Caudate	brain
44	chr2:101178200-101178400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr2:101178200-101178400	Enhancers	Fetal Muscle Leg	muscle
46	chr2:101178200-101178400	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr2:101178200-101178400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr2:101178200-101178400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr2:101178200-101178400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr2:101178200-101178400	Enhancers	Stomach Mucosa	stomach

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