Variant report

Variant	rs4652229
Chromosome Location	chr1:173846590-173846591
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173845188..173847906-chr1:173855416..173857290,2	MCF-7	breast:
2	chr1:173846395..173848405-chr1:173851384..173853662,2	MCF-7	breast:
3	chr1:173835892..173839551-chr1:173845916..173850195,7	K562	blood:
4	chr1:173800042..173801966-chr1:173845446..173848008,2	K562	blood:
5	chr1:173845893..173848745-chr1:173851379..173854012,4	K562	blood:
6	chr1:173846519..173848923-chr1:173855106..173856720,2	K562	blood:

Variant related genes	Relation type
ENSG00000234741	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12071594	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12071663	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12078824	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1322770	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1322775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322780	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799876	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2065171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5877	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5878	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7349095	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544605	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7552939	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9286895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941989	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425430	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425755	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425766	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661233	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 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	chr1:173838200-173846600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:173838200-173854200	Weak transcription	Gastric	stomach
3	chr1:173838200-173866000	Weak transcription	Small Intestine	intestine
4	chr1:173838400-173854200	Weak transcription	Esophagus	oesophagus
5	chr1:173838400-173854800	Weak transcription	Aorta	Aorta
6	chr1:173838400-173854800	Weak transcription	Right Ventricle	heart
7	chr1:173838400-173860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:173838600-173854800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:173838800-173855800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:173839000-173848400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:173839000-173850000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:173839000-173854800	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:173839000-173862800	Weak transcription	HMEC	breast
14	chr1:173839200-173850000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:173839200-173855000	Weak transcription	A549	lung
16	chr1:173839400-173847800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr1:173839400-173847800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:173839400-173849200	Strong transcription	Fetal Stomach	stomach
19	chr1:173839400-173850000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:173839600-173854600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:173840200-173849600	Strong transcription	Placenta	Placenta
22	chr1:173840200-173854200	Weak transcription	Colonic Mucosa	Colon
23	chr1:173840200-173854800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:173840200-173856800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:173840400-173855000	Weak transcription	Psoas Muscle	Psoas
26	chr1:173840600-173849400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:173840600-173854200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:173840800-173846600	Weak transcription	Fetal Thymus	thymus
29	chr1:173840800-173848400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:173840800-173854200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:173840800-173854200	Weak transcription	Brain Anterior Caudate	brain
32	chr1:173840800-173854200	Weak transcription	NHLF	lung
33	chr1:173840800-173854600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:173840800-173854600	Weak transcription	Hela-S3	cervix
35	chr1:173840800-173854800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:173840800-173854800	Weak transcription	Brain Angular Gyrus	brain
37	chr1:173840800-173855000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:173840800-173855000	Weak transcription	NHDF-Ad	bronchial
39	chr1:173841000-173847000	Weak transcription	HUVEC	blood vessel
40	chr1:173841000-173854800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:173841000-173854800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:173841000-173864400	Weak transcription	Fetal Heart	heart
43	chr1:173841000-173868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr1:173841200-173854800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:173841400-173849600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:173841600-173846600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:173841600-173847800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:173841800-173854800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:173841800-173854800	Weak transcription	K562	blood
50	chr1:173842000-173850000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links