Variant report

Variant	rs7042539
Chromosome Location	chr9:5830192-5830193
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:5828237..5830737-chr9:5830965..5832695,2	K562	blood:
2	chr9:5827878..5830835-chr9:6005826..6008939,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263575	Chromatin interaction
ENSG00000183354	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1141025	1.00[AMR][1000 genomes]
rs1260128	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1260130	0.81[AFR][1000 genomes]
rs1260134	1.00[AMR][1000 genomes]
rs1776008	0.84[AFR][1000 genomes]
rs2797512	0.81[AFR][1000 genomes]
rs2797516	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2797517	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6477001	0.83[AMR][1000 genomes]
rs6477002	1.00[AMR][1000 genomes]
rs7037680	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7042100	1.00[AMR][1000 genomes]
rs7046793	0.85[AFR][1000 genomes];1.00[AMR][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	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
3	nsv892151	chr9:5602528-5841438	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv3331803	chr9:5766129-5905103	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv1016365	chr9:5828435-5850834	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5779200-5832200	Weak transcription	Fetal Brain Male	brain
2	chr9:5784200-5831600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:5786800-5832200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:5787000-5830200	Weak transcription	Dnd41	blood
5	chr9:5787400-5832000	Weak transcription	Fetal Brain Female	brain
6	chr9:5787600-5831600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:5787600-5832000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:5787600-5832200	Weak transcription	Esophagus	oesophagus
9	chr9:5797400-5831400	Weak transcription	Psoas Muscle	Psoas
10	chr9:5798400-5831200	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:5799800-5831600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:5799800-5831800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:5799800-5831800	Weak transcription	HUVEC	blood vessel
14	chr9:5802200-5831200	Weak transcription	Colonic Mucosa	Colon
15	chr9:5802200-5831600	Weak transcription	Fetal Kidney	kidney
16	chr9:5802800-5831400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:5810200-5831800	Weak transcription	Brain Germinal Matrix	brain
18	chr9:5812000-5832200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:5813000-5832000	Weak transcription	NHDF-Ad	bronchial
20	chr9:5813200-5832200	Weak transcription	Lung	lung
21	chr9:5814600-5831800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:5816200-5831800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:5817800-5831800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr9:5818600-5832000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:5818600-5832200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:5818800-5830200	Weak transcription	Brain Anterior Caudate	brain
27	chr9:5819200-5831000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:5820800-5832200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:5822000-5830200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:5822000-5831800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:5823000-5831200	Weak transcription	Fetal Muscle Leg	muscle
32	chr9:5823400-5831400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr9:5823600-5831200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:5823800-5830400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr9:5824000-5831600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:5824200-5830400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr9:5824200-5831000	Weak transcription	Fetal Heart	heart
38	chr9:5824200-5831600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr9:5824400-5832000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr9:5824400-5832200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr9:5824600-5831800	Weak transcription	Fetal Stomach	stomach
42	chr9:5824800-5830400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr9:5824800-5831600	Weak transcription	Fetal Intestine Small	intestine
44	chr9:5824800-5832200	Weak transcription	Pancreas	Pancrea
45	chr9:5825200-5832200	Weak transcription	Placenta	Placenta
46	chr9:5825600-5830200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr9:5825600-5830200	Weak transcription	Thymus	Thymus
48	chr9:5825600-5830800	Weak transcription	Ovary	ovary
49	chr9:5825600-5831000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:5825600-5831000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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