Variant report

Variant	rs2143692
Chromosome Location	chr6:5190553-5190554
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	chr6:5189281..5191777-chr6:5204127..5205780,2	MCF-7	breast:
2	chr6:5149373..5152322-chr6:5189165..5191119,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10498665	0.82[JPT][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11242995	0.88[CHB][hapmap];0.82[JPT][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12190412	0.81[JPT][hapmap]
rs12660749	0.81[EUR][1000 genomes]
rs41302851	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4144009	0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4959336	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62385012	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6901828	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6934882	0.81[JPT][hapmap]
rs7740952	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7764853	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9791263	0.83[CHB][hapmap];0.87[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
3	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
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1022336	chr6:5145194-5200687	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1018984	chr6:5145194-5200801	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS 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	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5173000-5190800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:5175800-5193400	Weak transcription	Brain Substantia Nigra	brain
3	chr6:5176200-5190600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:5176200-5192400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:5176200-5201200	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:5176200-5203600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:5176200-5239600	Weak transcription	Thymus	Thymus
8	chr6:5177800-5205200	Weak transcription	Aorta	Aorta
9	chr6:5178400-5190800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:5179200-5207600	Weak transcription	Primary B cells from cord blood	blood
11	chr6:5179800-5190600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:5180000-5201000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:5180200-5212200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:5180400-5193200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:5180600-5192600	Weak transcription	Brain Angular Gyrus	brain
16	chr6:5180600-5195800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:5180600-5205000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:5180600-5205800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:5180600-5208200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:5181000-5190800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:5181200-5204600	Weak transcription	Esophagus	oesophagus
22	chr6:5182000-5196200	Weak transcription	Pancreas	Pancrea
23	chr6:5182000-5213600	Weak transcription	Gastric	stomach
24	chr6:5182200-5191400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:5182200-5200000	Weak transcription	Left Ventricle	heart
26	chr6:5184200-5192600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:5185200-5190800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:5186000-5192400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:5186400-5193600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:5186400-5195800	Weak transcription	K562	blood
31	chr6:5186400-5205000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:5186600-5190600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:5186600-5190800	Weak transcription	HepG2	liver
34	chr6:5186600-5191400	Weak transcription	Fetal Intestine Small	intestine
35	chr6:5186600-5196200	Weak transcription	Fetal Stomach	stomach
36	chr6:5186600-5200400	Weak transcription	Right Ventricle	heart
37	chr6:5186600-5202600	Weak transcription	Primary T cells from cord blood	blood
38	chr6:5187200-5194000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr6:5189000-5213200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr6:5189200-5190600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:5189400-5205400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:5189800-5190600	Enhancers	Brain Hippocampus Middle	brain
43	chr6:5189800-5192200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:5189800-5194000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:5190000-5190800	Enhancers	A549	lung
46	chr6:5190200-5191000	Enhancers	NH-A	brain
47	chr6:5190200-5191600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:5190200-5191800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:5190200-5191800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:5190200-5191800	Enhancers	HSMM	muscle

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