Variant report

Variant	rs4145561
Chromosome Location	chr6:13412841-13412842
allele	A/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	HDAC2	chr6:13412743-13413313	HepG2	liver:	n/a	n/a
2	HNF4A	chr6:13412798-13413231	HepG2	liver:	n/a	n/a
3	EP300	chr6:13412682-13413188	HepG2	liver:	n/a	chr6:13412840-13412853
4	RCOR1	chr6:13412771-13414043	HepG2	liver:	n/a	n/a
5	HNF4G	chr6:13412801-13413224	HepG2	liver:	n/a	n/a
6	SMC3	chr6:13412839-13413235	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:13412700-13414470	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:13412740-13413434	H1-neurons	neurons:	n/a	n/a
9	HEY1	chr6:13412787-13413241	HepG2	liver:	n/a	n/a
10	HDAC2	chr6:13412633-13413265	HepG2	liver:	n/a	n/a
11	ARID3A	chr6:13412810-13413187	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:13412779-13413436	H1-neurons	neurons:	n/a	n/a
13	NFIC	chr6:13412521-13413253	HepG2	liver:	n/a	n/a
14	MYBL2	chr6:13412681-13413429	HepG2	liver:	n/a	n/a
15	EP300	chr6:13412521-13413305	HepG2	liver:	n/a	chr6:13412840-13412853
16	HNF4G	chr6:13412740-13413295	HepG2	liver:	n/a	n/a
17	RAD21	chr6:13412824-13413137	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13407840..13410506-chr6:13411726..13413779,2	K562	blood:
2	chr6:13412824..13415397-chr6:13486120..13488724,2	MCF-7	breast:

Variant related genes	Relation type
GFOD1	TF binding region
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs487847	0.98[AFR][1000 genomes]
rs511992	0.83[YRI][hapmap]
rs541119	0.84[YRI][hapmap]
rs6458811	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13401800-13419000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:13405000-13418400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:13405000-13421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:13408600-13413000	Weak transcription	NHLF	lung
5	chr6:13408600-13413200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:13408600-13413200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:13408600-13413200	Weak transcription	Fetal Stomach	stomach
8	chr6:13408600-13413400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:13408600-13413400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr6:13408600-13413400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:13408600-13413400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:13408600-13413600	Weak transcription	Placenta	Placenta
13	chr6:13408600-13413600	Weak transcription	Osteobl	bone
14	chr6:13408600-13414200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:13408600-13414600	Weak transcription	NHEK	skin
16	chr6:13408600-13415800	Enhancers	Liver	Liver
17	chr6:13408600-13422600	Weak transcription	HSMM	muscle
18	chr6:13408800-13413200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:13408800-13413200	Weak transcription	Brain Anterior Caudate	brain
20	chr6:13408800-13413400	Weak transcription	NH-A	brain
21	chr6:13408800-13413600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:13408800-13413600	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr6:13408800-13414200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:13408800-13415200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:13408800-13419400	Weak transcription	Primary B cells from cord blood	blood
26	chr6:13408800-13420200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:13408800-13423000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:13409000-13413200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:13409000-13413400	Weak transcription	HMEC	breast
30	chr6:13409200-13414600	Weak transcription	Hela-S3	cervix
31	chr6:13409600-13415400	Enhancers	Brain Angular Gyrus	brain
32	chr6:13410000-13415000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:13410200-13415400	Enhancers	Brain Hippocampus Middle	brain
34	chr6:13410200-13415800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:13410400-13413800	Weak transcription	Fetal Brain Female	brain
36	chr6:13410400-13413800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr6:13410400-13416000	Enhancers	Brain Cingulate Gyrus	brain
38	chr6:13410400-13416400	Enhancers	Right Atrium	heart
39	chr6:13410600-13415600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:13410800-13416000	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr6:13411000-13415800	Enhancers	Psoas Muscle	Psoas
42	chr6:13411000-13415800	Weak transcription	GM12878-XiMat	blood
43	chr6:13411200-13413400	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:13411200-13415200	Enhancers	Adipose Nuclei	Adipose
45	chr6:13411400-13413000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:13411400-13413400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:13411400-13415600	Enhancers	Pancreas	Pancrea
48	chr6:13411400-13416200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:13411400-13419600	Weak transcription	Fetal Thymus	thymus
50	chr6:13411400-13421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links