Variant report

Variant	rs7955904
Chromosome Location	chr12:26427466-26427467
allele	G/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	EP300	chr12:26427325-26428060	GM12878	blood:	n/a	chr12:26428034-26428044 chr12:26427797-26427806
2	GATA3	chr12:26427198-26428186	MCF-7	breast:	n/a	chr12:26427487-26427494 chr12:26427482-26427498 chr12:26427480-26427501 chr12:26427487-26427494 chr12:26427876-26427885 chr12:26427487-26427494 chr12:26427485-26427494
3	JUND	chr12:26426839-26428137	K562	blood:	n/a	chr12:26427797-26427807 chr12:26427796-26427807 chr12:26427798-26427806 chr12:26427799-26427806
4	SIN3AK20	chr12:26427345-26428122	PANC-1	pancreas:	n/a	n/a
5	CTCF	chr12:26427340-26427610	NHEK	skin:	n/a	chr12:26427595-26427608
6	REST	chr12:26427294-26428064	PFSK-1	brain:	n/a	chr12:26427434-26427454
7	ZKSCAN1	chr12:26427339-26428066	Hela-S3	cervix:	n/a	n/a
8	TEAD4	chr12:26427255-26428110	K562	blood:	n/a	n/a
9	RCOR1	chr12:26427368-26428090	GM12878	blood:	n/a	n/a
10	JUND	chr12:26427128-26428273	SK-N-SH	brain:	n/a	chr12:26427797-26427807 chr12:26427796-26427807 chr12:26427798-26427806 chr12:26427799-26427806
11	RAD21	chr12:26427346-26428168	IMR90	lung:	n/a	n/a
12	GATA3	chr12:26427245-26428199	T-47D	breast:	n/a	chr12:26427487-26427494 chr12:26427482-26427498 chr12:26427480-26427501 chr12:26427487-26427494 chr12:26427876-26427885 chr12:26427487-26427494 chr12:26427485-26427494
13	CTCF	chr12:26427440-26427590	AG04450	lung:	n/a	n/a
14	JUND	chr12:26427404-26428072	Hela-S3	cervix:	n/a	chr12:26427797-26427807 chr12:26427796-26427807 chr12:26427798-26427806 chr12:26427799-26427806
15	MYC	chr12:26426491-26429208	NB4	blood:	n/a	chr12:26427797-26427806 chr12:26427798-26427807 chr12:26426664-26426673
16	NFIC	chr12:26427334-26428164	ECC-1	luminal epithelium:	n/a	n/a
17	SIN3AK20	chr12:26427333-26428004	A549	lung:	n/a	n/a
18	EP300	chr12:26427080-26428192	A549	lung:	n/a	chr12:26428034-26428044 chr12:26427797-26427806
19	GATA3	chr12:26427356-26427868	MCF-7	breast:	n/a	chr12:26427487-26427494 chr12:26427482-26427498 chr12:26427480-26427501 chr12:26427487-26427494 chr12:26427487-26427494 chr12:26427485-26427494
20	REST	chr12:26427328-26428224	PANC-1	pancreas:	n/a	chr12:26427434-26427454
21	GATA3	chr12:26426735-26428341	A549	lung:	n/a	chr12:26427487-26427494 chr12:26427079-26427086 chr12:26427482-26427498 chr12:26427077-26427087 chr12:26427480-26427501 chr12:26427487-26427494 chr12:26427876-26427885 chr12:26427077-26427086 chr12:26427076-26427088 chr12:26427487-26427494 chr12:26427485-26427494
22	GATA2	chr12:26427317-26428108	K562	blood:	n/a	chr12:26427484-26427498 chr12:26427487-26427494 chr12:26427482-26427498 chr12:26427480-26427501 chr12:26427487-26427494 chr12:26427876-26427885 chr12:26427487-26427494 chr12:26427485-26427494
23	JUND	chr12:26427325-26428197	MCF-7	breast:	n/a	chr12:26427797-26427807 chr12:26427796-26427807 chr12:26427798-26427806 chr12:26427799-26427806
24	TCF7L2	chr12:26426608-26428155	PANC-1	pancreas:	n/a	n/a
25	REST	chr12:26427289-26428089	PANC-1	pancreas:	n/a	chr12:26427434-26427454
26	POLR2A	chr12:26427137-26428900	U87	brain:	n/a	n/a
27	RAD21	chr12:26427425-26427889	GM12878	blood:	n/a	n/a
28	CTCF	chr12:26427440-26427590	BE2_C	brain:	n/a	n/a
29	POLR2A	chr12:26427415-26428069	HUVEC	blood vessel:	n/a	n/a
30	MAX	chr12:26427266-26428043	MCF-7	breast:	n/a	chr12:26427797-26427806 chr12:26427798-26427807
31	FOSL2	chr12:26427319-26428065	A549	lung:	n/a	chr12:26427797-26427807 chr12:26427798-26427806 chr12:26427799-26427806 chr12:26427795-26427806
32	EP300	chr12:26427459-26428025	MCF-7	breast:	n/a	chr12:26427797-26427806
33	GATA3	chr12:26427024-26428298	SK-N-SH	brain:	n/a	chr12:26427487-26427494 chr12:26427079-26427086 chr12:26427482-26427498 chr12:26427077-26427087 chr12:26427480-26427501 chr12:26427487-26427494 chr12:26427876-26427885 chr12:26427077-26427086 chr12:26427076-26427088 chr12:26427487-26427494 chr12:26427485-26427494
34	CEBPB	chr12:26427367-26428159	A549	lung:	n/a	n/a
35	MAX	chr12:26426820-26428285	A549	lung:	n/a	chr12:26427797-26427806 chr12:26427798-26427807
36	MAX	chr12:26427195-26428255	K562	blood:	n/a	chr12:26427797-26427806 chr12:26427798-26427807
37	RAD21	chr12:26427439-26427991	GM12878	blood:	n/a	n/a
38	E2F6	chr12:26427230-26428095	A549	lung:	n/a	n/a
39	RAD21	chr12:26427254-26428018	SK-N-SH_RA	brain:	n/a	n/a
40	CTCF	chr12:26427372-26427678	A549	lung:	n/a	chr12:26427595-26427608
41	JUND	chr12:26427203-26428185	SK-N-SH	brain:	n/a	chr12:26427797-26427807 chr12:26427796-26427807 chr12:26427798-26427806 chr12:26427799-26427806
42	NR2F2	chr12:26427389-26427983	MCF-7	breast:	n/a	n/a
43	ATF2	chr12:26427395-26428159	GM12878	blood:	n/a	n/a
44	HDAC2	chr12:26427312-26428117	MCF-7	breast:	n/a	n/a
45	POLR2A	chr12:26427361-26428228	IMR90	lung:	n/a	n/a
46	SPI1	chr12:26427303-26428160	GM12878	blood:	n/a	chr12:26427760-26427773
47	KAP1	chr12:26426619-26428103	HEK293	kidney:	n/a	chr12:26427796-26427805 chr12:26427613-26427621 chr12:26427054-26427062
48	BHLHE40	chr12:26426883-26428189	K562	blood:	n/a	n/a
49	RAD21	chr12:26427385-26427900	A549	lung:	n/a	n/a
50	MAX	chr12:26427236-26428182	SK-N-SH	brain:	n/a	chr12:26427797-26427806 chr12:26427798-26427807

No.	Distal block	Cell Line	Cell type
1	chr12:26340370..26340991-chr12:26427254..26427993,2	MCF-7	breast:
2	chr12:26397687..26399446-chr12:26426003..26429309,3	K562	blood:
3	chr12:26275957..26278285-chr12:26426218..26428121,2	MCF-7	breast:
4	chr12:26397649..26399446-chr12:26426022..26429309,3	K562	blood:
5	chr12:26272067..26272967-chr12:26427154..26428088,3	MCF-7	breast:
6	chr12:26266368..26268567-chr12:26426374..26428182,2	MCF-7	breast:
7	chr12:26427380..26429500-chr12:26439632..26442928,3	K562	blood:
8	chr12:26265923..26267917-chr12:26426739..26429196,2	K562	blood:
9	chr12:26427065..26429381-chr12:26431183..26432797,2	MCF-7	breast:
10	chr12:26417164..26419767-chr12:26425510..26427946,2	K562	blood:
11	chr12:26419878..26422720-chr12:26427079..26429529,2	K562	blood:

Variant related genes	Relation type
ENSG00000255750	TF binding region
ENSG00000123095	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10505994	1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10771272	0.83[ASN][1000 genomes]
rs12422927	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12423059	0.87[ASN][1000 genomes]
rs12426603	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1383115	0.88[EUR][1000 genomes]
rs1480039	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16915737	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16930376	0.86[ASN][1000 genomes]
rs17467456	0.92[EUR][1000 genomes]
rs34623765	0.86[ASN][1000 genomes]
rs55965428	0.81[ASN][1000 genomes]
rs7297586	1.00[YRI][hapmap]
rs73072448	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73072468	0.92[EUR][1000 genomes]
rs73072470	0.92[EUR][1000 genomes]
rs73072474	0.92[EUR][1000 genomes]
rs73072489	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817432	chr12:26355515-26873664	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv983496	chr12:26407082-26428038	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26421000-26429000	Enhancers	Fetal Intestine Small	intestine
2	chr12:26421800-26435800	Weak transcription	Gastric	stomach
3	chr12:26422600-26429200	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr12:26423800-26429000	Enhancers	HMEC	breast
5	chr12:26423800-26429200	Enhancers	Stomach Mucosa	stomach
6	chr12:26424000-26429000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:26424000-26429200	Enhancers	Fetal Intestine Large	intestine
8	chr12:26424000-26431800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:26424200-26429000	Enhancers	Fetal Muscle Leg	muscle
10	chr12:26424400-26428400	Enhancers	Right Atrium	heart
11	chr12:26424400-26430000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:26424600-26429000	Enhancers	Brain Substantia Nigra	brain
13	chr12:26424600-26429000	Enhancers	Duodenum Mucosa	Duodenum
14	chr12:26424600-26429000	Enhancers	Placenta	Placenta
15	chr12:26424600-26429000	Enhancers	Fetal Thymus	thymus
16	chr12:26424600-26429200	Enhancers	Brain Anterior Caudate	brain
17	chr12:26424600-26431800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:26424600-26433400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:26424800-26447000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr12:26425200-26427600	Enhancers	Stomach Smooth Muscle	stomach
21	chr12:26425400-26428200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr12:26425800-26431600	Enhancers	Primary hematopoietic stem cells	blood
23	chr12:26426000-26428200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:26426000-26429800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:26426000-26432200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr12:26426400-26429000	Enhancers	HSMM	muscle
27	chr12:26426400-26429200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:26426600-26428200	Enhancers	Brain Cingulate Gyrus	brain
29	chr12:26426600-26428200	Enhancers	Fetal Stomach	stomach
30	chr12:26426600-26428200	Enhancers	HSMMtube	muscle
31	chr12:26426600-26428400	Enhancers	Pancreas	Pancrea
32	chr12:26426600-26428600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr12:26426600-26429000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:26426600-26429000	Enhancers	Brain Angular Gyrus	brain
35	chr12:26426600-26429200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr12:26426600-26429200	Enhancers	Adipose Nuclei	Adipose
37	chr12:26426600-26429200	Enhancers	NHLF	lung
38	chr12:26426600-26431400	Enhancers	NHDF-Ad	bronchial
39	chr12:26426600-26431600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:26426600-26431800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:26426800-26427800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:26426800-26427800	Enhancers	Lung	lung
43	chr12:26426800-26427800	Enhancers	Right Ventricle	heart
44	chr12:26426800-26428000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:26426800-26428200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:26426800-26428200	Enhancers	Colon Smooth Muscle	Colon
47	chr12:26426800-26428200	Enhancers	Left Ventricle	heart
48	chr12:26426800-26428200	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr12:26426800-26428200	Flanking Active TSS	A549	lung
50	chr12:26426800-26428200	Flanking Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links