Variant report

Variant	rs2592955
Chromosome Location	chr4:129960040-129960041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129958375..129960190-chr4:129966439..129968736,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10014640	0.86[JPT][hapmap]
rs10028124	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10857134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12650832	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13132428	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1450727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699390	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699396	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1709416	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1709417	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757941	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs175964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs186444	0.85[JPT][hapmap]
rs1947269	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2167244	0.85[JPT][hapmap]
rs2218814	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2592953	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2592956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280592	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs280598	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280600	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280602	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2893267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099898	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3119696	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs318506	0.85[JPT][hapmap]
rs318509	0.85[JPT][hapmap]
rs318510	0.85[JPT][hapmap]
rs318512	0.86[JPT][hapmap]
rs318533	0.85[JPT][hapmap]
rs318535	0.85[JPT][hapmap]
rs318537	0.86[JPT][hapmap]
rs318538	0.89[JPT][hapmap]
rs318540	0.90[JPT][hapmap]
rs318542	0.85[JPT][hapmap]
rs318544	0.85[JPT][hapmap]
rs318546	0.85[JPT][hapmap]
rs318547	0.85[JPT][hapmap]
rs318548	0.86[JPT][hapmap]
rs318549	0.85[JPT][hapmap]
rs318554	0.90[JPT][hapmap]
rs318562	0.85[JPT][hapmap]
rs318564	0.86[JPT][hapmap]
rs337264	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs4165	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975192	0.90[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975287	0.86[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975288	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975289	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4975290	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975291	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975292	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs498435	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs536631	0.95[CEU][hapmap]
rs62316963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62318666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814109	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6817901	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6820403	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6820637	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6821814	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6830229	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6840358	0.86[JPT][hapmap]
rs7666529	0.85[JPT][hapmap]
rs7668762	0.84[JPT][hapmap]
rs7671455	0.88[AMR][1000 genomes]
rs7691218	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs789986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129937200-129964000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:129943200-129960200	Weak transcription	Primary B cells from cord blood	blood
3	chr4:129944400-129961000	Weak transcription	Primary T cells from cord blood	blood
4	chr4:129944600-129962800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr4:129944800-129965400	Weak transcription	Ovary	ovary
6	chr4:129945600-129981800	Weak transcription	Thymus	Thymus
7	chr4:129951200-129962400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr4:129951200-129967200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:129951400-129976200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:129953400-129962600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:129953600-129965600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:129953600-129965600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:129954800-129964400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr4:129955000-129960200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:129955000-129965200	Weak transcription	K562	blood
16	chr4:129955200-129961000	Weak transcription	GM12878-XiMat	blood
17	chr4:129956000-129962600	Weak transcription	HMEC	breast
18	chr4:129956400-129962200	Weak transcription	Fetal Lung	lung
19	chr4:129956600-129962400	Weak transcription	Left Ventricle	heart
20	chr4:129956800-129960800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:129956800-129960800	Weak transcription	HSMM	muscle
22	chr4:129956800-129962600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:129956800-129962600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr4:129957000-129963800	Weak transcription	Lung	lung
25	chr4:129957000-129965400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:129957400-129964400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:129957400-129964800	Weak transcription	Fetal Stomach	stomach
28	chr4:129958000-129961200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:129958400-129961600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:129958400-129964800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:129958600-129961600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr4:129958600-129961600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:129958600-129963000	Weak transcription	Psoas Muscle	Psoas
34	chr4:129958800-129961400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:129958800-129965400	Weak transcription	Adipose Nuclei	Adipose
36	chr4:129958800-129965400	Weak transcription	Liver	Liver
37	chr4:129958800-129966400	Weak transcription	Fetal Thymus	thymus
38	chr4:129959400-129961800	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:129959600-129961400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:129959800-129965600	Weak transcription	Fetal Intestine Small	intestine
41	chr4:129959800-129966000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:129960000-129961400	Strong transcription	Dnd41	blood
43	chr4:129960000-129962200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr4:129960000-129962400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr4:129960000-129962400	Weak transcription	Small Intestine	intestine
46	chr4:129960000-129964800	Weak transcription	Gastric	stomach

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