Variant report

Variant	rs6831869
Chromosome Location	chr4:57339441-57339442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57333435..57335762-chr4:57336689..57342030,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1140982	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1142851	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11934479	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11934636	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11940993	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12640212	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12643989	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12643996	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12644498	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12649799	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12650288	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1579019	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17086759	0.84[EUR][1000 genomes]
rs17086773	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17086801	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17086804	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17086830	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17086838	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17086868	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17086898	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17086909	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17086919	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17086922	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2271924	0.84[EUR][1000 genomes]
rs34398021	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34419325	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3733326	0.84[EUR][1000 genomes]
rs3796539	0.84[EUR][1000 genomes]
rs3796540	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3796549	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3796550	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4076103	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55909588	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56362514	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57245446	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58654038	0.84[EUR][1000 genomes]
rs59153415	0.84[EUR][1000 genomes]
rs59686671	0.80[AMR][1000 genomes]
rs59828502	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6830145	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7437839	0.85[EUR][1000 genomes]
rs7658340	0.86[AMR][1000 genomes]
rs7688482	0.96[AMR][1000 genomes];0.90[EUR][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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6831869	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57340200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:57334800-57340200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:57334800-57340200	Weak transcription	Left Ventricle	heart
4	chr4:57334800-57340200	Weak transcription	Small Intestine	intestine
5	chr4:57334800-57340200	Weak transcription	Spleen	Spleen
6	chr4:57334800-57353400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:57334800-57364000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
9	chr4:57335000-57340200	Weak transcription	Aorta	Aorta
10	chr4:57335000-57340800	Weak transcription	Colonic Mucosa	Colon
11	chr4:57335000-57354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:57335200-57340200	Weak transcription	Psoas Muscle	Psoas
13	chr4:57335200-57340200	Weak transcription	Right Ventricle	heart
14	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:57335600-57340200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:57335800-57354800	Weak transcription	Fetal Heart	heart
18	chr4:57335800-57359000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr4:57335800-57365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:57335800-57369200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:57336000-57340400	Strong transcription	K562	blood
24	chr4:57336000-57342200	Strong transcription	NH-A	brain
25	chr4:57336000-57347600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr4:57336000-57350000	Strong transcription	NHEK	skin
27	chr4:57336000-57362200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr4:57336000-57362600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:57336000-57364200	Strong transcription	Osteobl	bone
30	chr4:57336000-57369400	Strong transcription	Liver	Liver
31	chr4:57336000-57369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:57336000-57370000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:57336000-57370000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:57336200-57340800	Strong transcription	Fetal Kidney	kidney
37	chr4:57336200-57340800	Strong transcription	HMEC	breast
38	chr4:57336200-57346200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:57336200-57365000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:57336200-57369200	Strong transcription	Fetal Thymus	thymus
41	chr4:57336200-57370000	Strong transcription	Placenta	Placenta
42	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:57336400-57340200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:57336400-57342400	Strong transcription	Fetal Intestine Small	intestine
45	chr4:57336400-57342600	Strong transcription	Fetal Stomach	stomach
46	chr4:57336400-57342800	Strong transcription	Brain Germinal Matrix	brain
47	chr4:57336400-57345600	Strong transcription	HUVEC	blood vessel
48	chr4:57336400-57346400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:57336400-57346600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:57336400-57347000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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