Variant report

Variant	rs7793849
Chromosome Location	chr7:26249062-26249063
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	chr7:26249037..26251510-chr7:26254013..26255704,2	MCF-7	breast:
2	chr7:26248545..26251073-chr7:26252692..26255530,3	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11971108	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971308	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971320	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971402	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972057	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974685	1.00[ASN][1000 genomes]
rs11975011	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11976883	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11977822	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531642	1.00[CEU][hapmap]
rs12535874	0.82[CEU][hapmap]
rs17153176	1.00[CEU][hapmap]
rs17153183	1.00[CEU][hapmap]
rs17153193	1.00[CEU][hapmap]
rs17153217	0.82[CEU][hapmap]
rs17321514	1.00[ASN][1000 genomes]
rs17322608	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs28409739	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41275982	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55754901	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813103	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56021640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132015	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56273868	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56276467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56287413	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56376224	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56413126	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59142558	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59371106	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59685141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59820708	1.00[ASN][1000 genomes]
rs60411547	1.00[AMR][1000 genomes]
rs60954252	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61009175	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945071	0.82[CEU][hapmap]
rs6948113	1.00[ASN][1000 genomes]
rs73279689	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73279692	1.00[ASN][1000 genomes]
rs73281517	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281521	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281523	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281527	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281529	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281530	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281532	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281538	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281546	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281548	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281554	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281563	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281570	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281578	0.89[EUR][1000 genomes]
rs73281586	0.89[EUR][1000 genomes]
rs73281591	0.89[EUR][1000 genomes]
rs7793815	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794205	1.00[ASN][1000 genomes]
rs7798249	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7803860	1.00[ASN][1000 genomes]
rs7807030	1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021308	chr7:26116605-26419720	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv1018971	chr7:26161228-26380361	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	esv1821097	chr7:26243108-26303403	Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3433955	chr7:26248005-26251808	Genic enhancers Weak transcription Strong transcription Enhancers	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	n/a
5	esv3362501	chr7:26248077-26251791	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	n/a
6	esv3510561	chr7:26248090-26251747	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv3510562	chr7:26248090-26251747	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
8	esv3445760	chr7:26248117-26251331	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7793849	LTF	trans	brain	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26242400-26249400	Weak transcription	Stomach Mucosa	stomach
2	chr7:26242600-26249200	Weak transcription	Gastric	stomach
3	chr7:26242600-26249400	Weak transcription	Esophagus	oesophagus
4	chr7:26242800-26254000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:26243600-26249400	Weak transcription	Aorta	Aorta
6	chr7:26244200-26250000	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr7:26244400-26249200	Weak transcription	Brain Substantia Nigra	brain
8	chr7:26244400-26251400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:26244400-26271400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr7:26244800-26254200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr7:26245200-26252800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:26245400-26250600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:26245400-26250800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:26245400-26252200	Strong transcription	Fetal Lung	lung
15	chr7:26245400-26252800	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr7:26245400-26252800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr7:26245400-26252800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:26245400-26252800	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr7:26245400-26253000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:26245400-26253000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:26245400-26253200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:26245400-26253200	Strong transcription	HSMM	muscle
23	chr7:26245400-26253600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:26245600-26250200	Strong transcription	Colonic Mucosa	Colon
25	chr7:26245600-26251800	Strong transcription	Fetal Muscle Leg	muscle
26	chr7:26245600-26251800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:26245600-26253000	Strong transcription	Fetal Intestine Large	intestine
28	chr7:26245600-26253200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr7:26245600-26253600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:26245600-26253600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:26245600-26253600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr7:26245600-26253800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr7:26245800-26250200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr7:26245800-26252600	Strong transcription	HMEC	breast
35	chr7:26245800-26252800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr7:26245800-26252800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr7:26245800-26252800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:26245800-26252800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:26245800-26252800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:26245800-26253000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:26245800-26253000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr7:26245800-26253000	Strong transcription	Placenta	Placenta
43	chr7:26245800-26253200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr7:26245800-26253200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr7:26245800-26253200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr7:26245800-26254200	Strong transcription	Fetal Thymus	thymus
47	chr7:26245800-26257400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr7:26245800-26263400	Weak transcription	Fetal Brain Male	brain
49	chr7:26246000-26250600	Strong transcription	NHLF	lung
50	chr7:26246000-26250800	Strong transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links