Variant report

Variant	rs925241
Chromosome Location	chr4:126340996-126340997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:126340768..126341759-chr4:126443770..126444750,12	MCF-7	breast:
2	chr4:126340837..126341757-chr4:126443764..126444891,9	MCF-7	breast:
3	chr4:126235085..126238264-chr4:126339241..126343495,6	MCF-7	breast:
4	chr4:126340534..126341612-chr4:126443770..126444659,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196159	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10006602	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10010000	0.89[AFR][1000 genomes]
rs10025821	0.89[AFR][1000 genomes]
rs10025859	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10857105	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11932005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11941296	0.89[AFR][1000 genomes]
rs12650153	0.89[AFR][1000 genomes]
rs13119663	1.00[EUR][1000 genomes]
rs13132307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13144799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13144803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1354711	1.00[EUR][1000 genomes]
rs1354712	1.00[EUR][1000 genomes]
rs1395232	1.00[EUR][1000 genomes]
rs1395234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1395235	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1395242	1.00[EUR][1000 genomes]
rs1395243	0.89[AFR][1000 genomes]
rs1396687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1506356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1506358	1.00[EUR][1000 genomes]
rs1509293	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1509294	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1509295	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1509296	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1509297	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1509298	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1509301	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1553713	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1605825	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1605826	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1605827	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1911107	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1912041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1912042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1983118	1.00[EUR][1000 genomes]
rs2036723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2135428	0.89[AFR][1000 genomes]
rs2390835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2390840	0.89[AFR][1000 genomes]
rs28566737	1.00[EUR][1000 genomes]
rs4508902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4585321	0.89[AFR][1000 genomes]
rs4605670	0.89[AFR][1000 genomes]
rs4834030	0.89[AFR][1000 genomes]
rs4834032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4834033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4834034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4834036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4834037	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4834038	1.00[EUR][1000 genomes]
rs4834041	0.89[AFR][1000 genomes]
rs4834043	0.89[AFR][1000 genomes]
rs6534479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6816596	0.89[AFR][1000 genomes]
rs6833240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6851018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6851098	0.89[AFR][1000 genomes]
rs72914988	1.00[EUR][1000 genomes]
rs7656135	0.89[AFR][1000 genomes]
rs7656590	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7660088	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7660325	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7661810	0.89[AFR][1000 genomes]
rs7667605	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7675556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7678076	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7699122	0.89[AFR][1000 genomes]
rs958415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs958844	0.89[AFR][1000 genomes]
rs963397	0.89[AFR][1000 genomes]
rs988314	0.89[AFR][1000 genomes]
rs988863	0.89[AFR][1000 genomes]
rs988933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991326	0.89[AFR][1000 genomes]
rs9994836	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9996895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1006068	chr4:126103233-126497467	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830051	chr4:126234895-126403426	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv470070	chr4:126299145-126408586	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:126311800-126341800	Weak transcription	Fetal Heart	heart
2	chr4:126311800-126343600	Weak transcription	Fetal Stomach	stomach
3	chr4:126312000-126354400	Weak transcription	HSMM	muscle
4	chr4:126312200-126342800	Weak transcription	NHLF	lung
5	chr4:126316600-126354600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:126319000-126343800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:126320000-126343400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:126320200-126354400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:126320600-126344400	Weak transcription	Lung	lung
10	chr4:126324800-126344400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:126327000-126341800	Weak transcription	Right Ventricle	heart
12	chr4:126329000-126344000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:126329600-126344400	Weak transcription	Fetal Intestine Small	intestine
14	chr4:126329800-126341400	Weak transcription	NHDF-Ad	bronchial
15	chr4:126334600-126390400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:126335000-126343600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:126335000-126344000	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:126335200-126342000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:126335200-126353200	Weak transcription	Psoas Muscle	Psoas
20	chr4:126335200-126400800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:126335400-126343400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:126336000-126341000	Strong transcription	Ovary	ovary
23	chr4:126336000-126341400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:126336000-126343400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:126336400-126344400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:126336800-126344400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:126336800-126351000	Weak transcription	Fetal Brain Male	brain
28	chr4:126337000-126364400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr4:126337800-126341000	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:126337800-126356000	Weak transcription	Adipose Nuclei	Adipose
31	chr4:126337800-126356600	Weak transcription	Liver	Liver
32	chr4:126338000-126342200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:126338400-126342000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:126338400-126342600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:126338400-126353200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:126338600-126341800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:126338600-126342000	Weak transcription	HUVEC	blood vessel
38	chr4:126338600-126343600	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:126338600-126344000	Weak transcription	Fetal Brain Female	brain
40	chr4:126338600-126344400	Weak transcription	Aorta	Aorta
41	chr4:126338600-126371000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:126338800-126344200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr4:126338800-126344400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:126338800-126344400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:126338800-126371400	Weak transcription	Fetal Intestine Large	intestine
46	chr4:126339000-126355400	Weak transcription	Left Ventricle	heart
47	chr4:126340600-126342800	Enhancers	Fetal Kidney	kidney
48	chr4:126340800-126341000	Enhancers	Gastric	stomach
49	chr4:126340800-126341800	Weak transcription	Fetal Lung	lung

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