Variant report

Variant	rs17614442
Chromosome Location	chr6:144159200-144159201
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144152743..144156457-chr6:144158826..144162488,4	K562	blood:
2	chr6:144157133..144162462-chr6:144162661..144166157,6	MCF-7	breast:
3	chr6:144138025..144143695-chr6:144157697..144164178,7	K562	blood:
4	chr6:144159147..144162101-chr6:144162697..144165631,5	K562	blood:
5	chr6:144149084..144151621-chr6:144157302..144159967,3	K562	blood:

Variant related genes	Relation type
ENSG00000135521	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1061690	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963739	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11965439	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11966700	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11969396	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073137	0.86[JPT][hapmap]
rs17523460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328518	0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap]
rs2328521	0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap]
rs41285027	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55688549	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55911614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55971519	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56060230	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	esv3408554	chr6:144106707-144369589	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1034894	chr6:144148566-144170036	Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17614442	PHACTR2	cis	normal skin	skin_eQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144122200-144163600	Weak transcription	Colonic Mucosa	Colon
2	chr6:144122200-144163600	Weak transcription	Fetal Kidney	kidney
3	chr6:144125600-144163600	Weak transcription	Psoas Muscle	Psoas
4	chr6:144125800-144163600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:144128800-144163600	Weak transcription	HSMMtube	muscle
6	chr6:144129200-144159200	Weak transcription	HepG2	liver
7	chr6:144129200-144163600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:144129200-144163600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:144129600-144163600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:144130200-144163400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:144130200-144163800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:144130400-144159800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:144134000-144163800	Weak transcription	Aorta	Aorta
14	chr6:144134000-144163800	Weak transcription	Esophagus	oesophagus
15	chr6:144134000-144164000	Weak transcription	Gastric	stomach
16	chr6:144136600-144163600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr6:144140800-144163400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:144142200-144164000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:144143000-144163400	Weak transcription	Fetal Stomach	stomach
20	chr6:144144200-144160000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:144144200-144164000	Weak transcription	Lung	lung
22	chr6:144145200-144163600	Weak transcription	NH-A	brain
23	chr6:144145200-144163600	Weak transcription	NHEK	skin
24	chr6:144146200-144159200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:144146200-144163600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:144146400-144163600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:144146400-144163600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:144147800-144163400	Weak transcription	HUVEC	blood vessel
29	chr6:144150000-144163400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr6:144150000-144164000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:144150200-144160000	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:144150600-144159200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:144150600-144159600	Weak transcription	Liver	Liver
34	chr6:144150600-144163000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:144150800-144163600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr6:144150800-144163600	Weak transcription	Adipose Nuclei	Adipose
37	chr6:144150800-144163600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr6:144151800-144163600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:144153200-144163800	Weak transcription	Placenta	Placenta
40	chr6:144155400-144161600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:144157000-144163800	Weak transcription	Pancreas	Pancrea
42	chr6:144158800-144161000	Enhancers	Fetal Intestine Large	intestine
43	chr6:144158800-144161000	Enhancers	Fetal Intestine Small	intestine
44	chr6:144158800-144162200	Enhancers	Stomach Mucosa	stomach
45	chr6:144159200-144160400	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr6:144159200-144160600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr6:144159200-144160800	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links