Variant report

Variant	rs3190930
Chromosome Location	chr6:128291199-128291200
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	chr6:128290855..128292622-chr6:128292665..128294749,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1089653	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs35469349	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3933376	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs41285280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341027	1.00[JPT][hapmap]
rs4559105	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55743914	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7739912	1.00[JPT][hapmap]
rs802719	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs802725	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs802730	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs802731	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs802734	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs813915	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024516	chr6:128184182-128298278	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv604642	chr6:128278798-128351143	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3190930	TPD52L1	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128270600-128293400	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:128272400-128292600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:128278800-128297200	Weak transcription	Ovary	ovary
4	chr6:128280400-128304600	Weak transcription	Fetal Brain Male	brain
5	chr6:128281000-128293000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:128285200-128292600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:128285600-128307400	Weak transcription	Aorta	Aorta
8	chr6:128285800-128292200	Weak transcription	NHDF-Ad	bronchial
9	chr6:128286200-128292400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:128286200-128293000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:128286800-128297000	Weak transcription	Lung	lung
12	chr6:128287000-128292400	Weak transcription	NHEK	skin
13	chr6:128287000-128300200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:128287200-128292600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:128287200-128294200	Weak transcription	Fetal Intestine Small	intestine
16	chr6:128287200-128309000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:128287400-128293400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:128287400-128297200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:128287600-128292600	Weak transcription	Fetal Heart	heart
20	chr6:128287600-128292600	Weak transcription	Pancreas	Pancrea
21	chr6:128287600-128297200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:128287600-128308600	Weak transcription	Esophagus	oesophagus
23	chr6:128287800-128292600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr6:128287800-128292600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr6:128287800-128292600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr6:128287800-128292800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:128287800-128293200	Weak transcription	Brain Anterior Caudate	brain
28	chr6:128287800-128303600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:128288000-128293600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:128288000-128296400	Weak transcription	Brain Angular Gyrus	brain
31	chr6:128288000-128304800	Weak transcription	Stomach Mucosa	stomach
32	chr6:128288000-128307600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:128288200-128291400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr6:128288400-128291400	Strong transcription	HSMM	muscle
35	chr6:128288400-128292600	Weak transcription	HMEC	breast
36	chr6:128288600-128292400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:128288600-128292600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:128288600-128292600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr6:128288600-128293400	Weak transcription	Gastric	stomach
40	chr6:128288600-128297000	Weak transcription	Colonic Mucosa	Colon
41	chr6:128288600-128305400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr6:128288600-128306800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:128288600-128321800	Weak transcription	Small Intestine	intestine
44	chr6:128288800-128291400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:128288800-128291600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:128288800-128291600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:128288800-128291600	Strong transcription	Left Ventricle	heart
48	chr6:128288800-128293000	Weak transcription	Adipose Nuclei	Adipose
49	chr6:128288800-128293000	Weak transcription	NHLF	lung
50	chr6:128288800-128303800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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