Variant report

Variant	rs17138843
Chromosome Location	chr6:4784429-4784430
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	chr6:4778862..4780969-chr6:4783105..4785943,3	MCF-7	breast:
2	chr6:4675333..4676875-chr6:4782888..4785440,2	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs62384852	0.87[AFR][1000 genomes]
rs62384855	0.90[AFR][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	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3429586	chr6:4719363-4792438	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17138843	PRAMEF22	trans	lymphoblastoid	seeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4777800-4789000	Weak transcription	Pancreas	Pancrea
2	chr6:4778200-4785000	Weak transcription	Psoas Muscle	Psoas
3	chr6:4778200-4787000	Weak transcription	Thymus	Thymus
4	chr6:4778400-4785000	Weak transcription	Left Ventricle	heart
5	chr6:4778400-4785000	Weak transcription	Spleen	Spleen
6	chr6:4778400-4787000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:4778400-4787000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:4778400-4787000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:4778400-4789000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:4778400-4789600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:4778400-4790000	Weak transcription	Stomach Mucosa	stomach
12	chr6:4778600-4788800	Weak transcription	Adipose Nuclei	Adipose
13	chr6:4778600-4790000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:4780800-4786000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:4781200-4786800	Weak transcription	NHEK	skin
16	chr6:4781200-4788800	Weak transcription	HSMM	muscle
17	chr6:4781400-4794000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:4781400-4794400	Weak transcription	NHLF	lung
19	chr6:4781600-4797800	Weak transcription	Hela-S3	cervix
20	chr6:4781800-4785000	Weak transcription	Right Ventricle	heart
21	chr6:4781800-4785600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:4781800-4788200	Weak transcription	Ovary	ovary
23	chr6:4781800-4790000	Weak transcription	Fetal Lung	lung
24	chr6:4781800-4794200	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:4782000-4786000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:4782000-4790600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:4782000-4794400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:4782000-4797800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:4782400-4785400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr6:4782400-4785400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:4782400-4786400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:4782400-4787000	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:4782400-4788200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:4782400-4788800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:4782400-4788800	Weak transcription	Placenta	Placenta
36	chr6:4782600-4784800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:4782600-4785400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:4782600-4787000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:4782600-4788800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:4782600-4791400	Weak transcription	Fetal Heart	heart
41	chr6:4782800-4786600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:4782800-4787000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr6:4782800-4787000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:4782800-4789200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:4782800-4789600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:4782800-4790600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr6:4783000-4784600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:4783000-4786200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr6:4783000-4788800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:4783000-4789600	Weak transcription	Small Intestine	intestine

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