Variant report

Variant	rs6446554
Chromosome Location	chr4:6943292-6943293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:6908111..6910785-chr4:6941101..6945265,3	MCF-7	breast:
2	chr4:6911457..6914297-chr4:6942387..6944279,2	K562	blood:
3	chr4:6935997..6938458-chr4:6940561..6943507,2	K562	blood:
4	chr4:6942348..6944791-chr4:6958193..6960563,2	MCF-7	breast:
5	chr4:6940421..6944056-chr4:6949146..6952385,3	K562	blood:
6	chr4:6939325..6941725-chr4:6942990..6944855,2	K562	blood:
7	chr4:6941935..6944212-chr4:6988372..6991479,3	K562	blood:
8	chr4:6941810..6943426-chr4:6944150..6946769,2	K562	blood:

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10937767	1.00[AMR][1000 genomes]
rs10937773	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35375288	0.82[AFR][1000 genomes]
rs4234791	1.00[YRI][hapmap]
rs4327487	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs4376137	0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs4504252	0.83[AMR][1000 genomes]
rs4689058	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4689569	0.83[AMR][1000 genomes]
rs6446555	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446556	1.00[AMR][1000 genomes]
rs6446558	0.82[AFR][1000 genomes]
rs7655773	0.83[YRI][hapmap]
rs7661952	0.86[YRI][hapmap]
rs7675524	0.92[YRI][hapmap]
rs7689324	0.93[YRI][hapmap];0.82[AFR][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	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6928000-6969600	Weak transcription	Aorta	Aorta
2	chr4:6932000-6943400	Weak transcription	Fetal Brain Female	brain
3	chr4:6932000-6943400	Weak transcription	Fetal Kidney	kidney
4	chr4:6934400-6946400	Enhancers	Placenta	Placenta
5	chr4:6939000-6945600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr4:6939000-6946800	Enhancers	Adipose Nuclei	Adipose
7	chr4:6939200-6943400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:6939200-6943400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr4:6939200-6943800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:6939200-6946200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:6939200-6947000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:6939200-6947200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr4:6939200-6948000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr4:6939400-6943400	Enhancers	Primary B cells from cord blood	blood
15	chr4:6939400-6943600	Enhancers	Primary hematopoietic stem cells	blood
16	chr4:6939400-6943800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr4:6939400-6944200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr4:6939400-6945600	Enhancers	Primary B cells from peripheral blood	blood
19	chr4:6939600-6947000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:6939800-6945000	Enhancers	Brain Cingulate Gyrus	brain
21	chr4:6940600-6946400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr4:6940800-6944000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:6941000-6944000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:6941200-6943400	Enhancers	Primary T cells fromperipheralblood	blood
25	chr4:6941200-6945400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:6941200-6945800	Enhancers	Spleen	Spleen
27	chr4:6941400-6943400	Enhancers	Duodenum Mucosa	Duodenum
28	chr4:6941400-6943600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:6941400-6943800	Genic enhancers	Fetal Intestine Small	intestine
30	chr4:6941400-6944000	Enhancers	K562	blood
31	chr4:6941400-6946400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:6941400-6946400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:6941400-6947200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr4:6941600-6943400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr4:6941600-6944200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:6941600-6944200	Enhancers	Colonic Mucosa	Colon
37	chr4:6941600-6944600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr4:6941600-6945000	Enhancers	Fetal Muscle Leg	muscle
39	chr4:6941600-6945800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr4:6941600-6946800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:6941600-6947000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr4:6941800-6943400	Enhancers	Thymus	Thymus
43	chr4:6941800-6945400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:6941800-6947000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr4:6941800-6947000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr4:6941800-6947800	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr4:6942000-6943400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:6942000-6943400	Enhancers	Fetal Thymus	thymus
49	chr4:6942000-6943400	Enhancers	HMEC	breast
50	chr4:6942000-6943600	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links