Variant report

Variant	rs7250688
Chromosome Location	chr19:39459649-39459650
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	chr19:39459172..39462029-chr19:39880870..39883315,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006712	Chromatin interaction
ENSG00000063322	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10411224	1.00[EUR][1000 genomes]
rs10415871	1.00[EUR][1000 genomes]
rs10425811	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11881837	1.00[EUR][1000 genomes]
rs17883377	1.00[EUR][1000 genomes]
rs28414024	1.00[EUR][1000 genomes]
rs28422038	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28698570	1.00[EUR][1000 genomes]
rs28842622	1.00[EUR][1000 genomes]
rs58287865	1.00[EUR][1000 genomes]
rs6508831	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7252417	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73545566	1.00[EUR][1000 genomes]
rs73930246	1.00[EUR][1000 genomes]
rs8103029	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39441200-39465200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr19:39441200-39465200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:39441200-39465200	Weak transcription	NHLF	lung
4	chr19:39441200-39465400	Weak transcription	Right Atrium	heart
5	chr19:39441400-39462000	Weak transcription	Small Intestine	intestine
6	chr19:39441400-39465000	Weak transcription	HUVEC	blood vessel
7	chr19:39450000-39465400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:39453200-39465000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:39453200-39465000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr19:39453200-39465000	Weak transcription	K562	blood
11	chr19:39453200-39465200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:39453200-39465200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:39453200-39465200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:39453200-39465200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr19:39453200-39465800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:39453200-39465800	Weak transcription	Pancreas	Pancrea
17	chr19:39453400-39460600	Weak transcription	Adipose Nuclei	Adipose
18	chr19:39453400-39461200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:39453400-39464400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:39453400-39464800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:39453400-39464800	Weak transcription	Fetal Brain Male	brain
22	chr19:39453400-39464800	Weak transcription	Osteobl	bone
23	chr19:39453400-39465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr19:39453400-39465000	Weak transcription	HMEC	breast
25	chr19:39453400-39465200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:39453400-39465200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:39453400-39465200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:39453400-39465200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:39453400-39465200	Weak transcription	Aorta	Aorta
30	chr19:39453400-39465200	Weak transcription	Brain Angular Gyrus	brain
31	chr19:39453400-39465200	Weak transcription	HSMM	muscle
32	chr19:39453400-39465200	Weak transcription	NH-A	brain
33	chr19:39453400-39465200	Weak transcription	NHEK	skin
34	chr19:39453400-39465400	Weak transcription	Brain Anterior Caudate	brain
35	chr19:39453400-39465400	Weak transcription	Brain Germinal Matrix	brain
36	chr19:39453400-39465400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr19:39454000-39464600	Strong transcription	Fetal Stomach	stomach
38	chr19:39454200-39461400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:39454400-39465000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr19:39456000-39465600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:39456400-39462200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:39456400-39462200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:39457000-39459800	Strong transcription	Liver	Liver
44	chr19:39457000-39460800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr19:39457400-39460000	Strong transcription	HepG2	liver
46	chr19:39458000-39460000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:39458200-39460200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:39458600-39460200	Weak transcription	Fetal Muscle Leg	muscle
49	chr19:39458800-39465000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr19:39458800-39465000	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links