Variant report

Variant	rs13209954
Chromosome Location	chr6:4003922-4003923
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4002826..4004464-chr6:4017754..4020540,2	MCF-7	breast:
2	chr6:3999035..4001331-chr6:4003173..4005443,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRPF4B-3	chr6:4002154-4005104	NONHSAT107263

Variant related genes	Relation type
ENSG00000272248	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11751316	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13191877	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13191921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13199114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13204868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13205077	0.92[EUR][1000 genomes]
rs13207795	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214951	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13220367	0.92[EUR][1000 genomes]
rs35539914	0.83[EUR][1000 genomes]
rs35958400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	56 gene(s)	inside rSNPs	diseases
4	esv1800199	chr6:3986611-4014872	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3985400-4011000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:3991200-4008400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:3991200-4010400	Weak transcription	K562	blood
4	chr6:3991200-4011000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:3991200-4012200	Weak transcription	Left Ventricle	heart
6	chr6:3991400-4011000	Weak transcription	Lung	lung
7	chr6:3991400-4016800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:3991600-4007000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:3991600-4008000	Weak transcription	Liver	Liver
10	chr6:3991600-4008400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:3991600-4008400	Weak transcription	Fetal Kidney	kidney
12	chr6:3991600-4008400	Weak transcription	HSMM	muscle
13	chr6:3991600-4017200	Weak transcription	Fetal Brain Female	brain
14	chr6:3991600-4017400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:3991600-4017600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:3991800-4008000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:3991800-4016600	Weak transcription	Aorta	Aorta
18	chr6:3991800-4017400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:3991800-4017400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:3991800-4017600	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:3992600-4008400	Weak transcription	Fetal Intestine Small	intestine
22	chr6:3993200-4011000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:3997400-4016200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:3997400-4017400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:3997600-4017600	Weak transcription	Psoas Muscle	Psoas
26	chr6:3997800-4010800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:3997800-4011000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:3998000-4017400	Weak transcription	NHLF	lung
29	chr6:3998200-4017400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:3998400-4004400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:3998400-4005400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:3998400-4008200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:3998400-4008200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:3998400-4008400	Weak transcription	Brain Anterior Caudate	brain
35	chr6:3998400-4008400	Weak transcription	Fetal Lung	lung
36	chr6:3998400-4008400	Weak transcription	NHDF-Ad	bronchial
37	chr6:3998400-4016200	Weak transcription	Brain Germinal Matrix	brain
38	chr6:3998400-4017600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:3998400-4017600	Weak transcription	Small Intestine	intestine
40	chr6:3998600-4008400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:3998600-4008400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:3998600-4008400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:3998600-4012800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:3998800-4008200	Weak transcription	Osteobl	bone
45	chr6:3998800-4008400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:3998800-4008400	Weak transcription	NHEK	skin
47	chr6:3998800-4017400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:3999000-4004400	Weak transcription	Primary T cells from cord blood	blood
49	chr6:3999000-4004600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:3999000-4005400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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