Variant report

Variant	rs13430169
Chromosome Location	chr2:142888853-142888854
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr2:142887426-142889581	H1-neurons	neurons:	n/a	chr2:142888105-142888115
2	MAX	chr2:142888090-142889087	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr2:142888766-142889059	SK-N-SH	brain:	n/a	n/a
4	CHD1	chr2:142888716-142889277	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3AK20	chr2:142888760-142889119	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr2:142888035-142889284	Hela-S3	cervix:	n/a	n/a
7	SMC3	chr2:142887840-142889409	Hela-S3	cervix:	n/a	n/a
8	SMARCC2	chr2:142887473-142889383	Hela-S3	cervix:	n/a	chr2:142889119-142889128
9	POLR2A	chr2:142887897-142889482	Hela-S3	cervix:	n/a	n/a
10	MAX	chr2:142888263-142889091	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr2:142887748-142889013	MCF-7	breast:	n/a	n/a
12	POLR2A	chr2:142887853-142889198	HEK293	kidney:	n/a	n/a
13	ZKSCAN1	chr2:142888465-142889337	Hela-S3	cervix:	n/a	n/a
14	MAFK	chr2:142888371-142889353	H1-hESC	embryonic stem cell:	n/a	chr2:142889078-142889093 chr2:142889120-142889130 chr2:142889119-142889134 chr2:142889121-142889130
15	POLR2A	chr2:142888237-142889210	H1-neurons	neurons:	n/a	n/a
16	MXI1	chr2:142888307-142889367	Hela-S3	cervix:	n/a	n/a
17	CEBPB	chr2:142888577-142889338	IMR90	lung:	n/a	chr2:142889168-142889177 chr2:142889168-142889177 chr2:142889168-142889177
18	WRNIP1	chr2:142888561-142889032	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:142888332-142889342	SK-N-MC	brain:	n/a	n/a
20	USF2	chr2:142888627-142889171	Hela-S3	cervix:	n/a	n/a
21	MAX	chr2:142888419-142889054	H1-hESC	embryonic stem cell:	n/a	n/a
22	TAF1	chr2:142888802-142889026	H1-hESC	embryonic stem cell:	n/a	n/a
23	GTF2F1	chr2:142888338-142889395	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr2:142888420-142889230	PFSK-1	brain:	n/a	n/a
25	RFX5	chr2:142888235-142889377	Hela-S3	cervix:	n/a	n/a
26	CEBPB	chr2:142888016-142889603	Hela-S3	cervix:	n/a	chr2:142889168-142889177 chr2:142889168-142889177 chr2:142889168-142889177
27	KAP1	chr2:142887748-142889665	U2OS	brain:	n/a	n/a
28	POLR2A	chr2:142888181-142889335	Hela-S3	cervix:	n/a	n/a
29	ZNF143	chr2:142888403-142889255	Hela-S3	cervix:	n/a	n/a
30	SMARCC1	chr2:142887514-142889419	Hela-S3	cervix:	n/a	chr2:142889119-142889128
31	MAFF	chr2:142888832-142889308	HepG2	liver:	n/a	chr2:142889118-142889136
32	RAD21	chr2:142888790-142889278	H1-hESC	embryonic stem cell:	n/a	n/a
33	CHD2	chr2:142887910-142889313	Hela-S3	cervix:	n/a	n/a
34	EP300	chr2:142888487-142889373	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr2:142888230-142889413	U87	brain:	n/a	n/a
36	POLR2A	chr2:142887731-142888938	MCF-7	breast:	n/a	n/a
37	SMARCB1	chr2:142887536-142889347	Hela-S3	cervix:	n/a	chr2:142889119-142889128
38	SIN3A	chr2:142887607-142889256	H1-hESC	embryonic stem cell:	n/a	chr2:142888069-142888082
39	MAFK	chr2:142887872-142889379	Hela-S3	cervix:	n/a	chr2:142889078-142889093 chr2:142889120-142889130 chr2:142889119-142889134 chr2:142889121-142889130
40	POLR2A	chr2:142887608-142889138	H1-neurons	neurons:	n/a	n/a
41	KAP1	chr2:142887631-142889424	HEK293	kidney:	n/a	n/a
42	POLR2A	chr2:142887609-142889307	MCF-7	breast:	n/a	n/a
43	RCOR1	chr2:142888295-142889446	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr2:142888184-142889399	SK-N-MC	brain:	n/a	n/a
45	TCF7L2	chr2:142888415-142889310	HEK293	kidney:	n/a	n/a
46	CTBP2	chr2:142887504-142889036	H1-hESC	embryonic stem cell:	n/a	n/a
47	TAF1	chr2:142888683-142889314	H1-hESC	embryonic stem cell:	n/a	n/a
48	SIN3AK20	chr2:142888246-142889160	SK-N-SH	brain:	n/a	n/a
49	TCF7L2	chr2:142887726-142889312	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr2:142888023-142889401	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173835516..173837699-chr2:142887430..142889764,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRP1B-1	chr2:142888747-142889095	ENSG00000244125.1

Variant related genes	Relation type
LRP1B	TF binding region
ENSG00000185278	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10188131	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205625	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207741	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896128	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328304	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328797	0.87[AMR][1000 genomes]
rs13422148	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429243	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432762	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432866	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16856855	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59636122	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73963457	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73963462	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73963463	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9653181	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv875254	chr2:142833327-142931146	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006247	chr2:142851056-143289465	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142885400-142890800	Active TSS	Brain Anterior Caudate	brain
2	chr2:142885600-142890400	Active TSS	Brain Substantia Nigra	brain
3	chr2:142885800-142889800	Active TSS	Brain Angular Gyrus	brain
4	chr2:142885800-142890000	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr2:142886000-142890000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:142887200-142889000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:142887200-142889800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:142887400-142889200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:142887400-142889200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:142887400-142889200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr2:142887400-142889400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr2:142887400-142889400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:142887400-142889400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:142887400-142889400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr2:142887400-142889400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr2:142887400-142889600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr2:142887400-142889600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:142887400-142889600	Active TSS	Right Atrium	heart
19	chr2:142887600-142889000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr2:142887600-142889000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
21	chr2:142887600-142889200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:142887600-142889200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr2:142887600-142889200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
24	chr2:142887600-142889200	Bivalent/Poised TSS	Fetal Lung	lung
25	chr2:142887600-142889200	Active TSS	Gastric	stomach
26	chr2:142887600-142889200	Flanking Bivalent TSS/Enh	NHEK	skin
27	chr2:142887600-142889400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
28	chr2:142887600-142889400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:142887600-142889400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:142887600-142889400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:142887600-142889400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:142887600-142889400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
33	chr2:142887600-142889400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
34	chr2:142887600-142889400	Flanking Active TSS	HMEC	breast
35	chr2:142887600-142889400	Active TSS	NHLF	lung
36	chr2:142887600-142889600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr2:142887600-142889600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:142887600-142889600	Bivalent/Poised TSS	Fetal Kidney	kidney
39	chr2:142887600-142889800	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr2:142887800-142889000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:142887800-142889000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:142887800-142889000	Bivalent/Poised TSS	Psoas Muscle	Psoas
43	chr2:142887800-142889200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:142887800-142889200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:142887800-142889200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:142887800-142889200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
47	chr2:142887800-142889200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
48	chr2:142887800-142889200	Active TSS	Esophagus	oesophagus
49	chr2:142887800-142889200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
50	chr2:142887800-142889200	Bivalent/Poised TSS	Fetal Intestine Small	intestine

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