Variant report

Variant	rs5997427
Chromosome Location	chr22:29402539-29402540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29392383..29394290-chr22:29401537..29403639,2	MCF-7	breast:
2	chr22:29401603..29404388-chr22:29410754..29413254,2	K562	blood:
3	chr22:29395298..29397330-chr22:29401566..29403212,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16986909	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2347790	0.81[YRI][hapmap]
rs4333023	0.81[AFR][1000 genomes]
rs5762924	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs5762935	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6005956	0.85[YRI][hapmap]
rs713892	0.82[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs7290117	1.00[JPT][hapmap]
rs8139717	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9613777	0.83[MKK][hapmap];0.81[YRI][hapmap]
rs964589	0.81[YRI][hapmap]

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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5997427	EGFL6	trans	lymphoblastoid	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29398600-29402600	Enhancers	Pancreas	Pancrea
2	chr22:29398800-29405000	Weak transcription	HSMMtube	muscle
3	chr22:29399400-29403200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr22:29399600-29403400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr22:29400600-29412000	Weak transcription	A549	lung
6	chr22:29400600-29425400	Weak transcription	NHEK	skin
7	chr22:29400800-29405000	Weak transcription	Aorta	Aorta
8	chr22:29401000-29403600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr22:29401200-29403000	Enhancers	Duodenum Mucosa	Duodenum
10	chr22:29401200-29403200	Enhancers	Fetal Intestine Small	intestine
11	chr22:29401200-29403400	Enhancers	Fetal Intestine Large	intestine
12	chr22:29401200-29413400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr22:29401400-29403400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr22:29401400-29403400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr22:29401400-29405000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr22:29401400-29405000	Weak transcription	Ovary	ovary
17	chr22:29401400-29407200	Weak transcription	Right Atrium	heart
18	chr22:29401400-29414800	Weak transcription	Esophagus	oesophagus
19	chr22:29401400-29419200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr22:29401400-29425000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr22:29401600-29402600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr22:29401600-29402800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr22:29401600-29402800	Weak transcription	Fetal Kidney	kidney
24	chr22:29401600-29402800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr22:29401600-29403000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:29401600-29403200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr22:29401600-29403200	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr22:29401600-29403400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr22:29401600-29403800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr22:29401600-29404200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr22:29401600-29404200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr22:29401600-29404200	Weak transcription	Psoas Muscle	Psoas
33	chr22:29401600-29404800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr22:29401600-29405000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr22:29401600-29407000	Weak transcription	Brain Germinal Matrix	brain
36	chr22:29401600-29407000	Weak transcription	Brain Hippocampus Middle	brain
37	chr22:29401600-29407200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr22:29401600-29407600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr22:29401800-29402800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr22:29401800-29402800	Enhancers	HepG2	liver
41	chr22:29401800-29403400	Weak transcription	Left Ventricle	heart
42	chr22:29401800-29404200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr22:29401800-29404200	Weak transcription	Stomach Mucosa	stomach
44	chr22:29401800-29404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr22:29401800-29404400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr22:29401800-29406400	Weak transcription	Brain Substantia Nigra	brain
47	chr22:29401800-29406400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr22:29401800-29407000	Weak transcription	Fetal Lung	lung
49	chr22:29401800-29407200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr22:29401800-29407200	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links