Variant report

Variant	rs9841986
Chromosome Location	chr3:50620714-50620715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:
2	chr3:50619029..50623920-chr3:50628439..50631863,6	MCF-7	breast:
3	chr3:50378822..50381164-chr3:50619483..50621756,2	K562	blood:
4	chr3:50607065..50611118-chr3:50617412..50623416,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088543	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000114737	Chromatin interaction
ENSG00000004838	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13321914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17050997	1.00[AMR][1000 genomes]
rs17051020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051027	1.00[AMR][1000 genomes]
rs17051036	1.00[AMR][1000 genomes]
rs17051472	1.00[AMR][1000 genomes]
rs2085581	1.00[AMR][1000 genomes]
rs2232249	1.00[AMR][1000 genomes]
rs2232252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2355324	1.00[AMR][1000 genomes]
rs28496515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28525150	1.00[AMR][1000 genomes]
rs28546448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs736472	1.00[AMR][1000 genomes]
rs751850	1.00[AMR][1000 genomes]
rs762893	1.00[AMR][1000 genomes]
rs762894	1.00[AMR][1000 genomes]
rs9822071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9832171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9841390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9850032	1.00[AMR][1000 genomes]
rs9866852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50607400-50628200	Weak transcription	Small Intestine	intestine
2	chr3:50607600-50628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:50607800-50628200	Weak transcription	HSMMtube	muscle
4	chr3:50607800-50628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:50608000-50621400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:50608000-50621400	Weak transcription	HUVEC	blood vessel
7	chr3:50608000-50621800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:50608200-50624000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:50608200-50628400	Weak transcription	A549	lung
10	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
11	chr3:50608400-50625600	Weak transcription	NHDF-Ad	bronchial
12	chr3:50609200-50620800	Strong transcription	Brain Germinal Matrix	brain
13	chr3:50610000-50621400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:50610000-50623000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:50610200-50623600	Strong transcription	Fetal Muscle Leg	muscle
16	chr3:50610200-50624400	Strong transcription	Fetal Stomach	stomach
17	chr3:50610200-50628000	Weak transcription	Stomach Mucosa	stomach
18	chr3:50610400-50622400	Weak transcription	GM12878-XiMat	blood
19	chr3:50610400-50623200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:50610400-50623200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr3:50610400-50628400	Weak transcription	HSMM	muscle
22	chr3:50610600-50627600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:50611200-50621600	Strong transcription	Thymus	Thymus
24	chr3:50611400-50621600	Strong transcription	Fetal Intestine Small	intestine
25	chr3:50612200-50621400	Strong transcription	Fetal Intestine Large	intestine
26	chr3:50613000-50622400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr3:50613400-50621200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:50613400-50628000	Weak transcription	HMEC	breast
29	chr3:50613600-50621400	Strong transcription	Esophagus	oesophagus
30	chr3:50613800-50621200	Strong transcription	Brain Substantia Nigra	brain
31	chr3:50614400-50621800	Strong transcription	Dnd41	blood
32	chr3:50614600-50621800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:50614800-50620800	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:50615600-50621000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:50615800-50621800	Weak transcription	K562	blood
36	chr3:50616000-50625800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:50616000-50628600	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:50616600-50621600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:50617200-50622200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:50617400-50622000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:50617600-50620800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr3:50617600-50622400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:50617600-50626200	Enhancers	Liver	Liver
44	chr3:50617800-50628200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:50618000-50623200	Strong transcription	Fetal Muscle Trunk	muscle
46	chr3:50618000-50628000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:50618200-50626200	Enhancers	Right Ventricle	heart
48	chr3:50618200-50626800	Enhancers	Left Ventricle	heart
49	chr3:50618400-50621600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:50618600-50621200	Genic enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links