Variant report

Variant	rs489551
Chromosome Location	chr6:149689457-149689458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:149689327-149689697	GM12878	blood:	n/a	n/a
2	NFIC	chr6:149689068-149689867	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:149689075-149689672	GM12878	blood:	n/a	n/a
4	SMC3	chr6:149689183-149689538	GM12878	blood:	n/a	n/a
5	RUNX3	chr6:149689140-149689592	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:149689366-149689713	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149682033..149686160-chr6:149686843..149689832,5	K562	blood:

Variant related genes	Relation type
TAB2	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2143076	0.85[ASN][1000 genomes]
rs2262617	0.81[EUR][1000 genomes]
rs2789488	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2789492	0.85[ASN][1000 genomes]
rs4895788	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4897124	0.81[EUR][1000 genomes]
rs504985	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506268	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511100	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs514839	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs521845	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536203	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs537354	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540538	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs544947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560051	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562428	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564961	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577001	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579789	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580011	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585022	0.81[EUR][1000 genomes]
rs628488	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638407	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs652807	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6570965	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285519	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322178	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373589	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9373592	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9377210	0.81[AMR][1000 genomes]
rs9377212	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390677	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149656800-149694400	Weak transcription	Placenta	Placenta
2	chr6:149657800-149691200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:149658000-149695400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:149658200-149691000	Weak transcription	NHDF-Ad	bronchial
5	chr6:149658800-149692400	Weak transcription	Fetal Kidney	kidney
6	chr6:149659200-149691400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:149660400-149699200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:149662200-149694800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:149664000-149694400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:149667600-149691000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:149669400-149690400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:149674200-149691000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:149674600-149691800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:149674600-149699200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:149674600-149699200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:149674600-149699200	Weak transcription	Fetal Intestine Large	intestine
17	chr6:149677400-149692400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:149677800-149699200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:149680000-149692400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:149680000-149699200	Weak transcription	Fetal Brain Male	brain
21	chr6:149681000-149694800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:149681200-149699200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:149681600-149691000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:149681600-149691600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:149681800-149695000	Weak transcription	Adipose Nuclei	Adipose
26	chr6:149681800-149699200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:149682000-149691000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:149682200-149691200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:149682600-149699200	Weak transcription	Esophagus	oesophagus
30	chr6:149682600-149699200	Weak transcription	Spleen	Spleen
31	chr6:149682600-149709200	Weak transcription	Psoas Muscle	Psoas
32	chr6:149682800-149691000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:149682800-149691000	Weak transcription	Left Ventricle	heart
34	chr6:149682800-149692400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:149682800-149699200	Weak transcription	Lung	lung
36	chr6:149683200-149691200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:149683400-149698800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr6:149683600-149691000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:149683600-149691000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr6:149683600-149692400	Weak transcription	NH-A	brain
41	chr6:149683600-149699400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:149683800-149691000	Weak transcription	Fetal Muscle Leg	muscle
43	chr6:149684400-149698800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr6:149684600-149699200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:149685000-149689800	Enhancers	Colon Smooth Muscle	Colon
46	chr6:149685000-149690600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr6:149685000-149694000	Weak transcription	NHEK	skin
48	chr6:149685200-149694800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:149685200-149699200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr6:149685200-149699400	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links