Variant report

Variant	rs61370232
Chromosome Location	chr2:101180498-101180499
allele	A/G
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:8)
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	JUN	chr2:101178201-101180511	K562	blood:	n/a	chr2:101179689-101179698 chr2:101180362-101180373
2	POLR2A	chr2:101180414-101180522	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:101178955-101180617	K562	blood:	n/a	n/a
4	POLR2A	chr2:101180479-101180552	ProgFib	skin:	n/a	n/a
5	POLR2A	chr2:101178255-101180576	GM12878	blood:	n/a	n/a
6	HCFC1	chr2:101178640-101180603	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr2:101178771-101180629	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr2:101178337-101180558	GM12892	blood:	n/a	n/a
9	ZNF384	chr2:101179875-101180616	K562	blood:	n/a	n/a
10	POLR2A	chr2:101178909-101180536	GM12892	blood:	n/a	n/a
11	PAX5	chr2:101180300-101180566	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:101180208-101180653	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:101180241-101180752	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:101033038..101035627-chr2:101178228..101182939,5	K562	blood:
2	chr2:101177750..101180702-chr2:101616968..101620230,4	MCF-7	breast:
3	chr2:101032545..101035627-chr2:101179557..101182939,4	K562	blood:
4	chr2:101179725..101181553-chr2:101183212..101186603,3	K562	blood:
5	chr2:101177993..101180966-chr2:101192692..101194735,2	K562	blood:
6	chr2:101041152..101044058-chr2:101179314..101180934,2	K562	blood:
7	chr2:101177732..101180772-chr2:101616573..101620250,3	K562	blood:
8	chr2:101178645..101181337-chr2:101184679..101187696,4	MCF-7	breast:

No data

Variant related genes	Relation type
PDCL3	TF binding region
ENSG00000223947	Chromatin interaction
ENSG00000115539	Chromatin interaction
ENSG00000071082	Chromatin interaction
ENSG00000115526	Chromatin interaction
ENSG00000238328	Chromatin interaction
ENSG00000238029	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10178491	1.00[ASN][1000 genomes]
rs10190324	1.00[ASN][1000 genomes]
rs10200086	0.82[ASN][1000 genomes]
rs1052117	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114285	0.82[ASN][1000 genomes]
rs11681805	0.92[ASN][1000 genomes]
rs11691661	1.00[ASN][1000 genomes]
rs12469332	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12618862	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12622226	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13393125	0.82[ASN][1000 genomes]
rs13418741	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1401753	0.82[ASN][1000 genomes]
rs1533655	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2309848	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28560372	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28673254	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28694778	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2971007	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4850940	1.00[ASN][1000 genomes]
rs4851334	1.00[ASN][1000 genomes]
rs4851335	1.00[ASN][1000 genomes]
rs4851337	1.00[ASN][1000 genomes]
rs4851338	1.00[ASN][1000 genomes]
rs58420974	1.00[ASN][1000 genomes]
rs62155213	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66689046	0.82[ASN][1000 genomes]
rs67061569	1.00[ASN][1000 genomes]
rs6739992	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746622	0.93[AMR][1000 genomes]
rs6747613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748900	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753993	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557603	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560366	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594904	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596475	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]

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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101178400-101180600	Active TSS	Fetal Brain Female	brain
2	chr2:101178400-101180600	Active TSS	Osteobl	bone
3	chr2:101178400-101180800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:101178400-101180800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:101178600-101180600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr2:101178600-101180600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:101178600-101180600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:101178600-101180600	Active TSS	HSMM	muscle
9	chr2:101178600-101180600	Active TSS	NHLF	lung
10	chr2:101178800-101180600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:101178800-101180600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr2:101178800-101180600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr2:101178800-101180600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr2:101178800-101180600	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr2:101178800-101180600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:101178800-101180800	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr2:101178800-101180800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:101178800-101180800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:101178800-101180800	Active TSS	A549	lung
20	chr2:101178800-101181000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:101179000-101180800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:101179400-101180600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:101179800-101180600	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr2:101179800-101180600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:101179800-101180600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
26	chr2:101179800-101180800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr2:101180000-101180600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr2:101180000-101180600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:101180000-101180600	Active TSS	Brain Germinal Matrix	brain
30	chr2:101180000-101180600	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr2:101180000-101180800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:101180000-101180800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:101180000-101181600	Enhancers	Spleen	Spleen
34	chr2:101180200-101180600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:101180200-101180600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:101180200-101180600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:101180200-101180600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:101180200-101180600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr2:101180200-101180600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr2:101180200-101180600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:101180200-101180600	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr2:101180200-101180600	Flanking Active TSS	Colonic Mucosa	Colon
43	chr2:101180200-101180600	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr2:101180200-101180600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr2:101180200-101180600	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr2:101180200-101180600	Flanking Active TSS	Placenta	Placenta
47	chr2:101180200-101180600	Flanking Active TSS	Fetal Stomach	stomach
48	chr2:101180200-101180600	Enhancers	Placenta Amnion	Placenta Amnion
49	chr2:101180200-101180600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr2:101180200-101180600	Enhancers	Stomach Mucosa	stomach

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