Variant report

Variant	rs6544165
Chromosome Location	chr2:38733632-38733633
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38723600..38726002-chr2:38732894..38735725,2	MCF-7	breast:
2	chr2:38731728..38737474-chr2:38976694..38980031,6	K562	blood:
3	chr2:38699549..38701678-chr2:38732231..38735058,2	MCF-7	breast:
4	chr2:38731728..38734557-chr2:38977139..38980031,2	K562	blood:
5	chr2:38701267..38704004-chr2:38731920..38735874,3	K562	blood:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12614876	1.00[CEU][hapmap]
rs12616367	1.00[CEU][hapmap]
rs12619629	1.00[CEU][hapmap]
rs1543881	1.00[CEU][hapmap]
rs17576044	1.00[CEU][hapmap]
rs17603782	1.00[CEU][hapmap]
rs3765001	1.00[CEU][hapmap]
rs6760965	1.00[CEU][hapmap]
rs7579783	1.00[CEU][hapmap]
rs7584862	1.00[CEU][hapmap]
rs7606515	1.00[CEU][hapmap]

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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv522259	chr2:38668336-38736090	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv526489	chr2:38731774-38736090	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38729600-38735400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:38730000-38735800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:38731400-38735800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:38731600-38735600	Weak transcription	HSMMtube	muscle
5	chr2:38732600-38733800	Enhancers	Rectal Smooth Muscle	rectum
6	chr2:38733000-38733800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:38733000-38733800	Enhancers	Psoas Muscle	Psoas
8	chr2:38733200-38735400	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:38733200-38735400	Weak transcription	HepG2	liver
10	chr2:38733200-38735800	Weak transcription	Aorta	Aorta
11	chr2:38733200-38736200	Weak transcription	NHEK	skin
12	chr2:38733400-38735200	Weak transcription	NHLF	lung
13	chr2:38733400-38735400	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:38733400-38735400	Weak transcription	HMEC	breast
15	chr2:38733400-38735600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:38733400-38735600	Weak transcription	Ovary	ovary
17	chr2:38733400-38735600	Weak transcription	Right Atrium	heart
18	chr2:38733400-38735600	Weak transcription	NHDF-Ad	bronchial
19	chr2:38733400-38735800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:38733400-38736800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:38733600-38735000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:38733600-38735000	Weak transcription	Adipose Nuclei	Adipose
23	chr2:38733600-38735400	Weak transcription	Brain Anterior Caudate	brain
24	chr2:38733600-38735400	Weak transcription	Fetal Lung	lung
25	chr2:38733600-38735600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:38733600-38735600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:38733600-38735600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:38733600-38735600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:38733600-38735800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links