Variant report

Variant	rs3829337
Chromosome Location	chr12:58330053-58330054
allele	C/T
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	POU2F2	chr12:58329788-58330161	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:58329558-58330228	PANC-1	pancreas:	n/a	n/a
3	USF1	chr12:58329794-58330238	ECC-1	luminal epithelium:	n/a	chr12:58330020-58330031
4	TBP	chr12:58329145-58330234	K562	blood:	n/a	chr12:58329626-58329637
5	GABPA	chr12:58329581-58330332	A549	lung:	n/a	n/a
6	POLR2A	chr12:58329821-58330237	HepG2	liver:	n/a	n/a
7	JUND	chr12:58329690-58330168	A549	lung:	n/a	chr12:58329697-58329707 chr12:58329697-58329707 chr12:58329697-58329707
8	CHD2	chr12:58329735-58330170	Hela-S3	cervix:	n/a	n/a
9	ELF1	chr12:58329578-58330368	HCT-116	colon:	n/a	chr12:58329973-58329984 chr12:58329974-58329983 chr12:58329973-58329984
10	MAX	chr12:58329879-58330179	HepG2	liver:	n/a	n/a
11	TAF1	chr12:58329559-58330209	K562	blood:	n/a	n/a
12	GABPA	chr12:58329822-58330144	HepG2	liver:	n/a	n/a
13	GATA1	chr12:58329695-58330099	K562	blood:	n/a	chr12:58329696-58329705
14	IRF3	chr12:58330023-58330167	GM12878	blood:	n/a	n/a
15	GABPA	chr12:58329649-58330186	K562	blood:	n/a	n/a
16	POLR2A	chr12:58329155-58330889	MCF10A-Er-Src	breast:	n/a	n/a
17	YY1	chr12:58329897-58330116	HCT-116	colon:	n/a	n/a
18	CHD1	chr12:58329623-58330265	GM12878	blood:	n/a	n/a
19	ETS1	chr12:58329680-58330240	A549	lung:	n/a	chr12:58330001-58330010 chr12:58330001-58330010 chr12:58329971-58329981 chr12:58329973-58329982 chr12:58330001-58330010 chr12:58329994-58330010 chr12:58329970-58329986 chr12:58329973-58329982
20	FOXP2	chr12:58329853-58330117	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr12:58329580-58330728	MCF10A-Er-Src	breast:	n/a	n/a
22	TAF1	chr12:58329703-58330324	A549	lung:	n/a	n/a
23	ZNF143	chr12:58329368-58330192	K562	blood:	n/a	n/a
24	MYC	chr12:58329849-58330128	MCF-7	breast:	n/a	n/a
25	MAZ	chr12:58329682-58330219	GM12878	blood:	n/a	n/a
26	GATA1	chr12:58329261-58330758	PBDE	blood:	n/a	chr12:58329696-58329705
27	ELF1	chr12:58329609-58330212	K562	blood:	n/a	chr12:58329973-58329984 chr12:58329974-58329983 chr12:58329973-58329984
28	BCLAF1	chr12:58329603-58330222	GM12878	blood:	n/a	chr12:58329973-58329982 chr12:58329748-58329761
29	HDAC2	chr12:58329620-58330206	MCF-7	breast:	n/a	n/a
30	TAF1	chr12:58329851-58330139	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr12:58328665-58330602	K562	blood:	n/a	n/a
32	POLR2A	chr12:58329599-58330244	GM19193	blood:	n/a	n/a
33	POLR2A	chr12:58329595-58330421	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr12:58329606-58330210	GM12891	blood:	n/a	n/a
35	GABPA	chr12:58329664-58330253	MCF-7	breast:	n/a	n/a
36	POLR2A	chr12:58329704-58330194	HCT-116	colon:	n/a	n/a
37	CEBPB	chr12:58329764-58330133	K562	blood:	n/a	n/a
38	RCOR1	chr12:58329694-58330182	K562	blood:	n/a	n/a
39	SMC3	chr12:58329710-58330115	HepG2	liver:	n/a	n/a
40	POLR2A	chr12:58329727-58330238	MCF-7	breast:	n/a	n/a
41	SPI1	chr12:58329717-58330259	HL-60	blood:	n/a	n/a
42	TAF1	chr12:58329686-58330214	Hela-S3	cervix:	n/a	n/a
43	PBX3	chr12:58329750-58330215	A549	lung:	n/a	chr12:58330016-58330025
44	YY1	chr12:58329819-58330236	SK-N-SH_RA	brain:	n/a	n/a
45	CREB1	chr12:58329831-58330123	A549	lung:	n/a	n/a
46	HNF4G	chr12:58329792-58330144	HepG2	liver:	n/a	n/a
47	GATA3	chr12:58329538-58330075	SH-SY5Y	brain:	n/a	chr12:58329696-58329705
48	TCF12	chr12:58329765-58330132	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr12:58329698-58330245	A549	lung:	n/a	n/a
50	EP300	chr12:58329786-58330147	HepG2	liver:	n/a	chr12:58329978-58329994 chr12:58330002-58330009 chr12:58329974-58329981

No.	Distal block	Cell Line	Cell type
1	chr12:58003448..58005159-chr12:58329612..58331307,2	K562	blood:
2	chr12:58329287..58330059-chr5:130599325..130600170,2	NB4	blood:
3	chr12:58164032..58167803-chr12:58328284..58330655,5	K562	blood:
4	chr10:94607840..94608395-chr12:58329411..58330143,2	NB4	blood:
5	chr12:58238134..58241883-chr12:58327269..58331955,5	K562	blood:
6	chr12:57915577..57917168-chr12:58328157..58330221,2	K562	blood:
7	chr12:58236777..58241883-chr12:58327592..58331955,7	K562	blood:
8	chr12:58158495..58161066-chr12:58329095..58330993,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTDSP2-2	chr12:58329622-58330391	XLOC_010102
2	lnc-CTDSP2-2	chr12:58329624-58330625	NONHSAT028992

Variant related genes	Relation type
ENSG00000257698	TF binding region
ENSG00000111012	Chromatin interaction
ENSG00000158985	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000138190	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12816216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12822306	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12827346	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829858	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12830273	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12831787	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17120048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17120057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17120058	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17120198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120201	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17120203	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2888286	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2888287	0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34080411	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34142683	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34170251	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34221389	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34238095	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34300531	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34437870	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34499234	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34567504	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35326083	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35364486	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35375157	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35712620	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35726562	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56964775	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61015952	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61935800	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61935801	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581160	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581163	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7132343	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133275	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137226	0.83[ASN][1000 genomes]
rs7295307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7299512	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7303136	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7307628	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7962775	0.82[JPT][hapmap]
rs7968265	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7970948	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971139	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978519	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58327600-58330400	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr12:58327600-58330400	Active TSS	Thymus	Thymus
3	chr12:58328800-58330400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:58328800-58330800	Active TSS	K562	blood
5	chr12:58329000-58330200	Active TSS	HSMM	muscle
6	chr12:58329000-58330400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:58329000-58330400	Active TSS	Fetal Brain Male	brain
8	chr12:58329000-58330400	Active TSS	A549	lung
9	chr12:58329000-58330600	Active TSS	Brain Angular Gyrus	brain
10	chr12:58329200-58330200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:58329200-58330400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:58329200-58330400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:58329200-58330400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr12:58329200-58330400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr12:58329200-58330400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:58329200-58330400	Active TSS	Colon Smooth Muscle	Colon
17	chr12:58329200-58330400	Active TSS	NHLF	lung
18	chr12:58329200-58330600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:58329200-58330600	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr12:58329200-58330600	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr12:58329200-58330600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr12:58329200-58330600	Flanking Active TSS	Liver	Liver
23	chr12:58329200-58330600	Active TSS	Psoas Muscle	Psoas
24	chr12:58329200-58330600	Active TSS	Right Atrium	heart
25	chr12:58329200-58330600	Active TSS	Right Ventricle	heart
26	chr12:58329400-58330200	Active TSS	H1 Cell Line	embryonic stem cell
27	chr12:58329400-58330200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:58329400-58330200	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr12:58329400-58330200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:58329400-58330200	Active TSS	Aorta	Aorta
31	chr12:58329400-58330200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:58329400-58330200	Active TSS	Fetal Heart	heart
33	chr12:58329400-58330200	Active TSS	Fetal Muscle Trunk	muscle
34	chr12:58329400-58330200	Active TSS	Dnd41	blood
35	chr12:58329400-58330200	Active TSS	Hela-S3	cervix
36	chr12:58329400-58330400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:58329400-58330400	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr12:58329400-58330400	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr12:58329400-58330400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:58329400-58330400	Active TSS	Brain Anterior Caudate	brain
41	chr12:58329400-58330400	Active TSS	Brain Germinal Matrix	brain
42	chr12:58329400-58330400	Active TSS	Brain Hippocampus Middle	brain
43	chr12:58329400-58330400	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr12:58329400-58330400	Active TSS	Brain Substantia Nigra	brain
45	chr12:58329400-58330400	Active TSS	Fetal Brain Female	brain
46	chr12:58329400-58330400	Active TSS	Fetal Intestine Large	intestine
47	chr12:58329400-58330400	Active TSS	Fetal Kidney	kidney
48	chr12:58329400-58330400	Active TSS	Fetal Lung	lung
49	chr12:58329400-58330400	Active TSS	Fetal Muscle Leg	muscle
50	chr12:58329400-58330400	Active TSS	Fetal Stomach	stomach

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