Variant report

Variant	rs1699001
Chromosome Location	chr6:38606611-38606612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38565254..38567561-chr6:38606168..38608897,2	MCF-7	breast:
2	chr6:38605277..38607230-chr6:38608690..38610298,2	K562	blood:

Variant related genes	Relation type
ENSG00000183826	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10807196	0.96[CEU][hapmap]
rs10807198	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10947752	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1321056	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1699002	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1699003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699004	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1699005	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1699007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699017	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1739621	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1739626	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1739627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1739628	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1739629	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1739630	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1739632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1739633	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1781708	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1781711	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1781712	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1781738	0.85[EUR][1000 genomes]
rs1852979	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2144328	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252550	0.96[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2748172	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2814883	0.92[CEU][hapmap]
rs2814889	0.92[CEU][hapmap]
rs2814894	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4392718	0.96[CEU][hapmap]
rs6458059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs910516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394521	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38601200-38607000	Weak transcription	Gastric	stomach
2	chr6:38604200-38606800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr6:38605200-38607000	Weak transcription	Small Intestine	intestine
4	chr6:38605800-38606800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr6:38606200-38606800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:38606200-38606800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:38606200-38606800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:38606200-38606800	Flanking Active TSS	Fetal Heart	heart
9	chr6:38606200-38607000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:38606200-38607000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:38606200-38607000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr6:38606200-38607000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr6:38606200-38607000	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr6:38606200-38607000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:38606200-38607200	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr6:38606200-38608800	Active TSS	Right Atrium	heart
17	chr6:38606200-38609000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:38606400-38606800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:38606400-38606800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:38606400-38606800	Enhancers	Primary B cells from peripheral blood	blood
21	chr6:38606400-38606800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:38606400-38606800	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr6:38606400-38606800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr6:38606400-38607000	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr6:38606400-38607000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr6:38606400-38607000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr6:38606400-38607000	Flanking Active TSS	HMEC	breast
28	chr6:38606400-38607000	Flanking Active TSS	NHDF-Ad	bronchial
29	chr6:38606400-38607200	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr6:38606400-38607200	Flanking Active TSS	HUVEC	blood vessel
31	chr6:38606400-38607400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:38606400-38607400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:38606400-38608400	Active TSS	NHLF	lung
34	chr6:38606400-38608600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:38606400-38608800	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr6:38606400-38608800	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr6:38606600-38606800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
38	chr6:38606600-38606800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:38606600-38606800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:38606600-38606800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
41	chr6:38606600-38606800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:38606600-38606800	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr6:38606600-38606800	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr6:38606600-38606800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr6:38606600-38606800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:38606600-38606800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:38606600-38606800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:38606600-38606800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:38606600-38606800	Enhancers	Aorta	Aorta
50	chr6:38606600-38606800	Flanking Active TSS	Brain Cingulate Gyrus	brain

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