Variant report

Variant	rs6438530
Chromosome Location	chr3:119179387-119179388
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1060569	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13080905	0.98[ASN][1000 genomes]
rs1797839	0.86[ASN][1000 genomes]
rs1900742	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919590	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1976919	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2030816	0.86[AMR][1000 genomes]
rs2177812	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814397	0.86[ASN][1000 genomes]
rs4687855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687860	0.98[ASN][1000 genomes]
rs4688005	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688008	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688014	0.85[ASN][1000 genomes]
rs6414282	0.96[ASN][1000 genomes]
rs6414283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6438529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438535	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6777535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6778945	0.88[ASN][1000 genomes]
rs6794822	0.96[ASN][1000 genomes]
rs6796970	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7621259	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628626	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7630587	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9289129	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9809155	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836326	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9836627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850447	0.88[ASN][1000 genomes]
rs9867768	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs9873196	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9874480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119147200-119180400	Weak transcription	Stomach Mucosa	stomach
2	chr3:119148800-119180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:119149400-119181000	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:119149400-119181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:119150400-119180200	Strong transcription	Fetal Intestine Large	intestine
6	chr3:119150600-119180800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:119152000-119179800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:119152200-119179400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:119154000-119181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:119158000-119180000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:119158800-119180000	Strong transcription	Adipose Nuclei	Adipose
12	chr3:119158800-119180000	Strong transcription	Dnd41	blood
13	chr3:119159800-119179400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:119159800-119180800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:119160400-119179400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr3:119160400-119180200	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr3:119160600-119180000	Strong transcription	HUVEC	blood vessel
18	chr3:119160600-119180800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:119160800-119179400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:119161000-119180800	Weak transcription	Fetal Brain Male	brain
21	chr3:119161200-119179600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:119161800-119180000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:119161800-119180400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:119162600-119181000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:119163200-119179800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr3:119163200-119180400	Strong transcription	HSMM	muscle
27	chr3:119163200-119180800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:119163200-119180800	Strong transcription	Placenta	Placenta
29	chr3:119163200-119181000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:119163400-119180400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:119163400-119180800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:119163400-119180800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:119163400-119180800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:119163400-119181200	Strong transcription	Fetal Thymus	thymus
35	chr3:119163600-119180400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:119163600-119180600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr3:119163800-119179800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:119163800-119180800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr3:119164200-119180800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr3:119165400-119180000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:119167200-119179400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:119168600-119180600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:119169600-119180400	Strong transcription	Primary B cells from cord blood	blood
44	chr3:119170600-119180400	Strong transcription	HSMMtube	muscle
45	chr3:119170800-119180800	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:119171000-119179600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:119171000-119179600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:119171000-119180200	Strong transcription	K562	blood
49	chr3:119171200-119180200	Strong transcription	HMEC	breast
50	chr3:119171200-119180800	Strong transcription	Brain Germinal Matrix	brain

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