Variant report

Variant	rs4400619
Chromosome Location	chr1:222729986-222729987
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222723739..222728526-chr1:222728539..222731564,4	K562	blood:
2	chr1:222724484..222728107-chr1:222728855..222732774,4	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11485178	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11485180	0.96[EUR][1000 genomes]
rs11487813	0.96[EUR][1000 genomes]
rs1319392	0.96[EUR][1000 genomes]
rs1603742	0.96[EUR][1000 genomes]
rs17163214	0.95[EUR][1000 genomes]
rs17463531	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17509774	1.00[ASN][1000 genomes]
rs1909192	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1995152	0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2133185	0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2173401	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2378583	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2936027	1.00[ASW][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2936031	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2936034	0.94[EUR][1000 genomes]
rs2936035	0.92[EUR][1000 genomes]
rs2936037	0.88[EUR][1000 genomes]
rs2936038	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2936040	0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2936048	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3002131	1.00[ASN][1000 genomes]
rs3002151	0.93[EUR][1000 genomes]
rs3008641	0.96[EUR][1000 genomes]
rs3008644	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3008650	0.91[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs34457750	1.00[ASN][1000 genomes]
rs34747518	1.00[ASN][1000 genomes]
rs35458674	1.00[ASN][1000 genomes]
rs35932524	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873203	chr1:222332906-222775000	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv2762168	chr1:222717698-222736854	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4400619	MAP4K4	trans	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222720400-222730200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:222720400-222732200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:222720400-222733800	Weak transcription	Fetal Kidney	kidney
4	chr1:222720600-222730200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:222720800-222734000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:222720800-222742400	Weak transcription	NHLF	lung
7	chr1:222720800-222757400	Weak transcription	HSMMtube	muscle
8	chr1:222721000-222733000	Weak transcription	NH-A	brain
9	chr1:222721200-222762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:222721400-222730400	Weak transcription	HMEC	breast
11	chr1:222721400-222730800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:222721600-222730200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:222721800-222762400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:222722000-222730600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:222722000-222730600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:222722000-222745000	Weak transcription	Hela-S3	cervix
17	chr1:222722000-222755600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:222722000-222755800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:222723800-222742400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:222724000-222730000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:222724000-222733400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:222724800-222750800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:222725200-222733600	Weak transcription	Colonic Mucosa	Colon
24	chr1:222725600-222762200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:222726200-222730400	Weak transcription	GM12878-XiMat	blood
26	chr1:222726200-222731000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:222726600-222730000	Weak transcription	NHDF-Ad	bronchial
28	chr1:222726600-222736800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:222726800-222730400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:222727200-222737200	Strong transcription	Primary B cells from cord blood	blood
31	chr1:222727400-222732400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:222727600-222730600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:222727600-222737400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:222727600-222762600	Weak transcription	Aorta	Aorta
35	chr1:222727800-222731200	Enhancers	Liver	Liver
36	chr1:222727800-222732400	Weak transcription	Brain Angular Gyrus	brain
37	chr1:222727800-222733000	Weak transcription	Right Ventricle	heart
38	chr1:222727800-222762400	Weak transcription	Thymus	Thymus
39	chr1:222728000-222732400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:222728000-222744400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:222728200-222730600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:222728200-222731000	Strong transcription	HSMM	muscle
43	chr1:222728200-222762200	Weak transcription	Small Intestine	intestine
44	chr1:222728400-222730600	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:222728400-222737400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:222728400-222738600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr1:222728600-222730800	Strong transcription	Fetal Brain Male	brain
48	chr1:222728600-222731200	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:222728600-222731800	Strong transcription	Fetal Brain Female	brain
50	chr1:222728600-222737000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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