Variant report

Variant	rs55794458
Chromosome Location	chr12:12534799-12534800
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12534486..12536460-chr12:12761134..12763160,2	MCF-7	breast:
2	chr12:12532395..12535127-chr12:12868296..12871166,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111276	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs58932972	1.00[AFR][1000 genomes]
rs7303326	0.84[AFR][1000 genomes]
rs74062518	1.00[AFR][1000 genomes]
rs7966625	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7976922	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1036040	chr12:12506839-12541869	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1037542	chr12:12506839-12542868	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1045637	chr12:12506839-12546747	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv1052243	chr12:12512726-12541869	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv1051597	chr12:12513364-12541869	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv557584	chr12:12514203-12541869	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv818893	chr12:12515184-12541869	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv1042425	chr12:12519319-12540455	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv1050133	chr12:12519319-12541869	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv1049869	chr12:12519319-12542868	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv1047762	chr12:12520906-12541869	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
15	esv2760275	chr12:12530073-12546759	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv557585	chr12:12530718-12541869	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv818894	chr12:12530718-12541869	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv437141	chr12:12530718-12544266	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	esv3483107	chr12:12531330-12542599	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	esv3483096	chr12:12531345-12542593	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	esv3483118	chr12:12531345-12542593	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	esv3483085	chr12:12531375-12542582	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv557586	chr12:12532984-12540702	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv557587	chr12:12532984-12541212	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	nsv557588	chr12:12532984-12541407	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	nsv557589	chr12:12532984-12541683	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
27	nsv557590	chr12:12532984-12541787	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
28	nsv557591	chr12:12532984-12541841	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
29	esv2421794	chr12:12532984-12541869	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
30	nsv469115	chr12:12532984-12541869	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
31	nsv469117	chr12:12532984-12541869	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
32	nsv469118	chr12:12532984-12541869	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
33	nsv557592	chr12:12532984-12541869	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
34	nsv557593	chr12:12532984-12543233	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
35	nsv818895	chr12:12532984-12544266	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
36	nsv517152	chr12:12532984-12547645	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12511400-12535000	Weak transcription	Esophagus	oesophagus
2	chr12:12511400-12537800	Weak transcription	HSMMtube	muscle
3	chr12:12511400-12540600	Weak transcription	HSMM	muscle
4	chr12:12511600-12540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:12511600-12550600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:12512000-12545000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:12512200-12540400	Weak transcription	HMEC	breast
8	chr12:12512400-12540600	Weak transcription	Psoas Muscle	Psoas
9	chr12:12516200-12537600	Weak transcription	Dnd41	blood
10	chr12:12516400-12535200	Weak transcription	Lung	lung
11	chr12:12516400-12540000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:12519200-12549800	Weak transcription	Aorta	Aorta
13	chr12:12519400-12537400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:12519600-12540400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:12519800-12537600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:12520200-12535000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:12521000-12538000	Weak transcription	Left Ventricle	heart
18	chr12:12521800-12542800	Weak transcription	Adipose Nuclei	Adipose
19	chr12:12521800-12556200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr12:12525400-12550200	Weak transcription	Fetal Stomach	stomach
21	chr12:12526000-12541600	Weak transcription	Brain Germinal Matrix	brain
22	chr12:12526400-12535400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:12526400-12537800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:12526400-12540400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:12526400-12540400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:12526600-12537600	Weak transcription	K562	blood
28	chr12:12526800-12535000	Weak transcription	Primary B cells from cord blood	blood
29	chr12:12526800-12537600	Weak transcription	Small Intestine	intestine
30	chr12:12526800-12538000	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:12529400-12537600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:12529600-12541400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:12529800-12535200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr12:12530000-12535000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:12530800-12534800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:12530800-12536200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:12530800-12537600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:12531400-12534800	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr12:12531600-12539000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr12:12532400-12537400	Enhancers	HepG2	liver
41	chr12:12532400-12540000	Weak transcription	NHEK	skin
42	chr12:12532600-12534800	Enhancers	Liver	Liver
43	chr12:12532600-12534800	Enhancers	Stomach Mucosa	stomach
44	chr12:12532800-12535000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:12532800-12556400	Weak transcription	Spleen	Spleen
46	chr12:12533000-12535000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:12533000-12535000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:12533000-12535200	Weak transcription	Fetal Intestine Large	intestine
49	chr12:12533000-12537200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:12533000-12537800	Weak transcription	H1 Cell Line	embryonic stem cell

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