Variant report

Variant	rs835591
Chromosome Location	chr12:50451742-50451743
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	MXI1	chr12:50450578-50451858	IMR90	lung:	n/a	n/a
2	CTCF	chr12:50449519-50451803	A549	lung:	n/a	chr12:50449938-50449956 chr12:50451041-50451050 chr12:50451664-50451677 chr12:50449933-50449954 chr12:50451252-50451265 chr12:50451667-50451680 chr12:50451391-50451404 chr12:50451060-50451073
3	MAX	chr12:50450534-50451748	A549	lung:	n/a	chr12:50451390-50451400 chr12:50450863-50450873
4	ZBTB7A	chr12:50450967-50452040	ECC-1	luminal epithelium:	n/a	n/a
5	SIN3A	chr12:50450517-50451744	H1-hESC	embryonic stem cell:	n/a	chr12:50451628-50451641
6	MAX	chr12:50450546-50451764	K562	blood:	n/a	chr12:50451390-50451400 chr12:50450863-50450873
7	REST	chr12:50450613-50451808	H1-neurons	neurons:	n/a	n/a
8	MXI1	chr12:50449506-50452883	SK-N-SH	brain:	n/a	n/a
9	SMC3	chr12:50449323-50451865	SK-N-SH	brain:	n/a	chr12:50449940-50449954
10	CTCF	chr12:50449287-50452309	SK-N-SH	brain:	n/a	chr12:50449938-50449956 chr12:50451041-50451050 chr12:50451664-50451677 chr12:50449933-50449954 chr12:50451252-50451265 chr12:50451667-50451680 chr12:50451391-50451404 chr12:50451060-50451073
11	MAZ	chr12:50450656-50451928	IMR90	lung:	n/a	chr12:50451390-50451400
12	MAX	chr12:50450487-50451793	ECC-1	luminal epithelium:	n/a	chr12:50451390-50451400 chr12:50450863-50450873
13	YY1	chr12:50451129-50451798	HepG2	liver:	n/a	chr12:50451268-50451277 chr12:50451269-50451283 chr12:50451268-50451282 chr12:50451663-50451677 chr12:50451383-50451394 chr12:50451372-50451383
14	ZBTB7A	chr12:50451425-50451779	K562	blood:	n/a	n/a
15	ZBTB7A	chr12:50450638-50452129	ECC-1	luminal epithelium:	n/a	n/a
16	HMGN3	chr12:50451164-50451756	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50450867..50453197-chr12:50472058..50474772,2	MCF-7	breast:
2	chr12:50450859..50453547-chr12:50463168..50465511,2	MCF-7	breast:
3	chr12:50450302..50454051-chr12:50467339..50469182,3	K562	blood:
4	chr12:50417982..50420791-chr12:50450221..50452010,2	MCF-7	breast:
5	chr12:50360734..50361410-chr12:50451208..50452167,2	MCF-7	breast:
6	chr12:50451739..50453323-chr12:50478566..50480871,2	MCF-7	breast:
7	chr12:50360045..50361666-chr12:50451717..50454140,2	MCF-7	breast:
8	chr12:50348029..50350628-chr12:50451106..50452724,2	MCF-7	breast:

Variant related genes	Relation type
ASIC1	TF binding region
ENSG00000161800	Chromatin interaction
ENSG00000257378	Chromatin interaction
ENSG00000086159	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs376184	0.85[ASN][1000 genomes]
rs386469	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs393848	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs404751	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs439171	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs450423	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs484951	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs590460	0.92[ASN][1000 genomes]
rs613066	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs627869	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs627887	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs653576	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs685012	0.80[ASN][1000 genomes]
rs706789	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs706794	0.85[ASN][1000 genomes]
rs835593	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs835594	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836184	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs836185	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs836186	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs844359	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs860699	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50449600-50452200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:50449800-50452000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr12:50450600-50451800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
4	chr12:50450800-50451800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:50450800-50451800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
6	chr12:50450800-50451800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:50450800-50452000	Active TSS	Aorta	Aorta
8	chr12:50450800-50452000	Active TSS	Brain Substantia Nigra	brain
9	chr12:50450800-50452200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr12:50450800-50452400	Bivalent/Poised TSS	Thymus	Thymus
11	chr12:50451000-50451800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:50451000-50451800	Active TSS	HSMMtube	muscle
13	chr12:50451000-50452000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:50451000-50452000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:50451000-50452000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:50451000-50452000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr12:50451000-50452000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:50451000-50452000	Active TSS	Brain Hippocampus Middle	brain
19	chr12:50451000-50452000	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr12:50451000-50452000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:50451000-50452000	Active TSS	Colon Smooth Muscle	Colon
22	chr12:50451000-50452000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
23	chr12:50451000-50452000	Active TSS	Fetal Brain Female	brain
24	chr12:50451000-50452000	Active TSS	Psoas Muscle	Psoas
25	chr12:50451000-50452000	Active TSS	A549	lung
26	chr12:50451000-50452200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr12:50451000-50452200	Active TSS	Brain Angular Gyrus	brain
28	chr12:50451000-50452600	Active TSS	Brain Cingulate Gyrus	brain
29	chr12:50451000-50452800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr12:50451200-50451800	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:50451200-50451800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:50451200-50451800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:50451200-50451800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:50451200-50451800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr12:50451200-50451800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:50451200-50451800	Active TSS	Muscle Satellite Cultured Cells	--
37	chr12:50451200-50451800	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr12:50451200-50451800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:50451200-50451800	Active TSS	Duodenum Mucosa	Duodenum
40	chr12:50451200-50451800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr12:50451200-50451800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
42	chr12:50451200-50451800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
43	chr12:50451200-50451800	Bivalent/Poised TSS	Placenta	Placenta
44	chr12:50451200-50451800	Active TSS	Gastric	stomach
45	chr12:50451200-50451800	Active TSS	Left Ventricle	heart
46	chr12:50451200-50451800	Active TSS	Lung	lung
47	chr12:50451200-50451800	Active TSS	Pancreas	Pancrea
48	chr12:50451200-50451800	Active TSS	Placenta Amnion	Placenta Amnion
49	chr12:50451200-50451800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
50	chr12:50451200-50451800	Active TSS	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links