Variant report

Variant	rs2764150
Chromosome Location	chr6:5032260-5032261
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	chr6:5004308..5006000-chr6:5030652..5032441,2	K562	blood:
2	chr6:5002773..5004480-chr6:5029318..5032794,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPP40-1	chr6:5031990-5034916	ENSG00000248284

Variant related genes	Relation type
ENSG00000124787	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1108040	0.89[ASN][1000 genomes]
rs1108041	0.92[ASN][1000 genomes]
rs11967778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11967814	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1627212	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17139235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1749155	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1771868	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1771873	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1771874	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1815673	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1815674	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1815675	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2002380	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2147705	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2764128	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2764131	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2764133	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2764140	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2764144	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2764147	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764153	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764154	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764170	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2764189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793239	0.83[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs2793246	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2793252	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793253	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793254	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793256	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793257	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793258	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2985677	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2994695	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2994696	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4246072	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4281005	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57793325	0.81[ASN][1000 genomes]
rs62385142	0.81[ASN][1000 genomes]
rs62385148	0.88[ASN][1000 genomes]
rs707964	0.87[GIH][hapmap]
rs726743	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs754334	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs811259	0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs877229	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378925	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2764150	FOXF2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5027000-5032600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:5027000-5032800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:5027000-5032800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:5027000-5033000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:5027000-5033000	Weak transcription	Colonic Mucosa	Colon
6	chr6:5027000-5033200	Weak transcription	Esophagus	oesophagus
7	chr6:5027000-5036400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:5027200-5032600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:5027200-5032600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:5027200-5032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:5027200-5032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:5027200-5032800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:5027200-5032800	Weak transcription	HMEC	breast
14	chr6:5027200-5033000	Weak transcription	Fetal Intestine Small	intestine
15	chr6:5027200-5033000	Weak transcription	Right Atrium	heart
16	chr6:5027200-5034600	Weak transcription	Fetal Thymus	thymus
17	chr6:5027200-5047200	Weak transcription	Adipose Nuclei	Adipose
18	chr6:5027400-5032800	Weak transcription	Fetal Stomach	stomach
19	chr6:5027400-5033200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:5029400-5034200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:5029800-5033000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:5030600-5034200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:5030800-5032800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:5031000-5032600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:5031000-5034400	Weak transcription	Osteobl	bone
26	chr6:5031200-5033200	Weak transcription	Right Ventricle	heart
27	chr6:5031200-5034000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:5031200-5034200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:5031200-5042800	Weak transcription	Ovary	ovary
30	chr6:5031400-5032600	Weak transcription	HUVEC	blood vessel
31	chr6:5031400-5032600	Weak transcription	NHEK	skin
32	chr6:5031400-5036400	Weak transcription	K562	blood
33	chr6:5031600-5032600	Weak transcription	HepG2	liver
34	chr6:5031600-5032800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:5031600-5033000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:5031600-5033000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:5031600-5033000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:5031600-5033000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:5031600-5033000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:5031600-5034000	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:5031600-5034200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:5031600-5034200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:5031600-5042800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:5031800-5033000	Weak transcription	Placenta	Placenta
45	chr6:5031800-5034200	Weak transcription	Thymus	Thymus
46	chr6:5031800-5043800	Weak transcription	Spleen	Spleen
47	chr6:5032000-5033000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:5032000-5033000	Weak transcription	Fetal Muscle Trunk	muscle

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