Variant report

Variant	rs4549
Chromosome Location	chr3:42636141-42636142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42632973..42636724-chr3:42645956..42649361,3	MCF-7	breast:
2	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
3	chr3:42603400..42605797-chr3:42635471..42638332,2	MCF-7	breast:
4	chr3:42635009..42637446-chr3:42638784..42643768,7	MCF-7	breast:
5	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs2136012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271181	0.86[EUR][1000 genomes]
rs2271185	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271186	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2976533	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339658	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339723	0.82[AMR][1000 genomes]
rs339725	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339726	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339727	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339728	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs339733	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs342507	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs342508	0.84[CHD][hapmap]
rs342521	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342522	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342536	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342537	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774398	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs586082	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs587712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597498	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs607568	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612733	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs614323	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs617722	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs627664	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs638836	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs639692	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs640689	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6441892	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs663673	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs689251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs704979	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8351	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs925457	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9865109	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4549	NKTR	cis	parietal	SCAN
rs4549	NKTR	cis	Nerve Tibial	GTEx
rs4549	NKTR	cis	Muscle Skeletal	GTEx
rs4549	TMEM42	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42633200-42641400	Weak transcription	Aorta	Aorta
2	chr3:42633200-42641600	Weak transcription	Gastric	stomach
3	chr3:42633400-42636400	Strong transcription	Fetal Muscle Leg	muscle
4	chr3:42633400-42641200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:42633400-42641200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:42633400-42641200	Weak transcription	HSMMtube	muscle
7	chr3:42633400-42641400	Weak transcription	Ovary	ovary
8	chr3:42633400-42641400	Weak transcription	Psoas Muscle	Psoas
9	chr3:42633400-42641400	Weak transcription	Right Ventricle	heart
10	chr3:42633400-42641600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:42633400-42641600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:42633400-42641600	Weak transcription	Esophagus	oesophagus
13	chr3:42633400-42641600	Weak transcription	Spleen	Spleen
14	chr3:42633600-42636400	Strong transcription	Fetal Lung	lung
15	chr3:42633600-42636800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:42633600-42637000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:42633600-42637600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:42633600-42638000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:42633600-42639200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:42633600-42639400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:42633600-42641200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:42633600-42641200	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:42633600-42641200	Weak transcription	Fetal Kidney	kidney
24	chr3:42633600-42641200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:42633600-42641200	Weak transcription	Right Atrium	heart
26	chr3:42633600-42641200	Weak transcription	NHEK	skin
27	chr3:42633600-42641400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:42633600-42641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:42633600-42641400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:42633600-42641600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:42633600-42641600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:42633600-42641600	Weak transcription	Pancreas	Pancrea
33	chr3:42633800-42638600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:42633800-42638800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:42633800-42641200	Weak transcription	Brain Germinal Matrix	brain
36	chr3:42634000-42641200	Weak transcription	Fetal Intestine Small	intestine
37	chr3:42634000-42641600	Weak transcription	Lung	lung
38	chr3:42634200-42637400	Strong transcription	Placenta	Placenta
39	chr3:42634200-42638800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:42634400-42641200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:42634600-42641200	Weak transcription	Fetal Brain Male	brain
42	chr3:42634800-42636400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr3:42634800-42636400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
44	chr3:42634800-42636600	Strong transcription	HUVEC	blood vessel
45	chr3:42634800-42636800	Strong transcription	Fetal Intestine Large	intestine
46	chr3:42634800-42638000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr3:42634800-42638200	Strong transcription	Fetal Thymus	thymus
48	chr3:42635000-42636400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:42635000-42636400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:42635000-42636400	Strong transcription	NHDF-Ad	bronchial

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