Variant report

Variant	rs10049998
Chromosome Location	chr4:7923973-7923974
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7921981..7926079-chr4:7940006..7943093,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs11932843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13115701	0.94[ASN][1000 genomes]
rs13131154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13137140	0.94[ASN][1000 genomes]
rs13140004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13145572	0.94[ASN][1000 genomes]
rs13146302	0.94[ASN][1000 genomes]
rs13147998	0.87[ASN][1000 genomes]
rs1320073	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13435273	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17770177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2067842	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs2385902	0.88[CHB][hapmap]
rs28394221	0.94[ASN][1000 genomes]
rs28492032	0.80[AMR][1000 genomes]
rs28539821	0.94[ASN][1000 genomes]
rs28546404	0.94[ASN][1000 genomes]
rs28605531	0.94[ASN][1000 genomes]
rs28613311	0.85[ASN][1000 genomes]
rs28631977	0.89[ASN][1000 genomes]
rs28673208	0.94[ASN][1000 genomes]
rs28688265	0.94[ASN][1000 genomes]
rs28754920	0.94[ASN][1000 genomes]
rs2891927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34072304	0.89[ASN][1000 genomes]
rs34075381	0.94[ASN][1000 genomes]
rs34092549	0.94[ASN][1000 genomes]
rs34119140	0.89[ASN][1000 genomes]
rs34121576	0.94[ASN][1000 genomes]
rs34132874	0.89[ASN][1000 genomes]
rs34181918	0.94[ASN][1000 genomes]
rs34189407	0.94[ASN][1000 genomes]
rs34221000	0.94[ASN][1000 genomes]
rs34383852	0.94[ASN][1000 genomes]
rs34392913	0.94[ASN][1000 genomes]
rs34570748	0.93[ASN][1000 genomes]
rs34598003	0.89[ASN][1000 genomes]
rs34652148	0.94[ASN][1000 genomes]
rs34712341	0.94[ASN][1000 genomes]
rs34868842	0.94[ASN][1000 genomes]
rs34869495	0.82[ASN][1000 genomes]
rs34909423	0.89[ASN][1000 genomes]
rs34982807	0.89[ASN][1000 genomes]
rs35114566	0.84[ASN][1000 genomes]
rs35138920	0.94[ASN][1000 genomes]
rs35152796	0.94[ASN][1000 genomes]
rs35154266	0.94[ASN][1000 genomes]
rs35238070	0.94[ASN][1000 genomes]
rs35349192	0.94[ASN][1000 genomes]
rs35502845	0.94[ASN][1000 genomes]
rs35727635	0.94[ASN][1000 genomes]
rs35735994	0.94[ASN][1000 genomes]
rs35881667	0.93[ASN][1000 genomes]
rs35905776	0.94[ASN][1000 genomes]
rs35933973	0.86[ASN][1000 genomes]
rs35967175	0.94[ASN][1000 genomes]
rs36013696	0.94[ASN][1000 genomes]
rs36046241	0.90[ASN][1000 genomes]
rs36106793	0.94[ASN][1000 genomes]
rs3934540	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap]
rs4234831	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs4256209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4296663	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4361385	1.00[ASW][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.89[ASN][1000 genomes]
rs4411970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4443285	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4447865	1.00[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs4487321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4579115	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs4689860	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4689865	0.81[JPT][hapmap]
rs4689875	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4696742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696747	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696762	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696772	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4696827	0.82[CHD][hapmap]
rs62289341	0.91[ASN][1000 genomes]
rs62289351	0.91[ASN][1000 genomes]
rs6446625	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6446627	1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.82[ASN][1000 genomes]
rs6446629	0.86[ASW][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[ASN][1000 genomes]
rs6824266	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.94[ASN][1000 genomes]
rs6826598	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6828574	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829505	0.94[ASN][1000 genomes]
rs6832352	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6833054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6837845	0.94[ASN][1000 genomes]
rs6838055	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6845014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6855982	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6856371	0.81[JPT][hapmap]
rs6856795	0.86[ASW][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap]
rs71600561	0.90[ASN][1000 genomes]
rs71601887	0.94[ASN][1000 genomes]
rs71601888	0.94[ASN][1000 genomes]
rs71601889	0.94[ASN][1000 genomes]
rs71601890	0.94[ASN][1000 genomes]
rs71601892	0.94[ASN][1000 genomes]
rs7660568	0.94[ASN][1000 genomes]
rs7667982	0.86[CHD][hapmap]
rs7682202	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs7682611	1.00[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7683285	0.84[JPT][hapmap]
rs7691386	0.94[ASN][1000 genomes]
rs7694106	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7697255	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
3	chr4:7909200-7925400	Weak transcription	Hela-S3	cervix
4	chr4:7912000-7931200	Weak transcription	Aorta	Aorta
5	chr4:7912800-7931200	Weak transcription	Gastric	stomach
6	chr4:7913000-7927600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:7913000-7930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:7913000-7931000	Weak transcription	Fetal Intestine Large	intestine
9	chr4:7913200-7926400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:7913600-7926200	Weak transcription	Fetal Brain Female	brain
11	chr4:7913600-7927200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:7913600-7930400	Weak transcription	NHEK	skin
13	chr4:7913800-7925600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:7914000-7926800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:7914200-7925800	Weak transcription	HSMMtube	muscle
16	chr4:7914200-7930800	Weak transcription	Fetal Kidney	kidney
17	chr4:7914400-7925600	Weak transcription	HSMM	muscle
18	chr4:7915000-7926000	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:7915000-7928200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:7915000-7930400	Weak transcription	Fetal Lung	lung
21	chr4:7918800-7930400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:7919000-7925600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:7919000-7925800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:7919000-7929000	Weak transcription	Brain Germinal Matrix	brain
25	chr4:7919200-7930600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:7919400-7926200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:7919600-7925800	Weak transcription	Fetal Heart	heart
28	chr4:7919600-7930800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:7919800-7924800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:7919800-7925600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:7919800-7926200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:7919800-7930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:7919800-7931200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr4:7920000-7924200	Weak transcription	Pancreas	Pancrea
35	chr4:7920000-7925800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:7920000-7925800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:7920000-7926000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:7920000-7926400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:7920200-7925800	Weak transcription	NHLF	lung
40	chr4:7920200-7926400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:7920400-7926400	Weak transcription	Fetal Intestine Small	intestine
42	chr4:7920400-7926400	Weak transcription	Right Atrium	heart
43	chr4:7920600-7931200	Weak transcription	Lung	lung
44	chr4:7921000-7926400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr4:7921000-7930600	Weak transcription	Esophagus	oesophagus
46	chr4:7921200-7924600	Weak transcription	A549	lung
47	chr4:7921200-7925200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr4:7921200-7925400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr4:7921200-7926000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:7921200-7926000	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links