Variant report

Variant	rs6794677
Chromosome Location	chr3:121423495-121423496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121417854..121420828-chr3:121422749..121424314,2	K562	blood:
2	chr3:121422713..121424587-chr3:121439673..121442209,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12631824	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13067629	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1492177	0.86[EUR][1000 genomes]
rs1574655	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1574735	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1873645	0.87[EUR][1000 genomes]
rs1919552	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1919557	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1986351	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1986874	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2001390	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2001391	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2070179	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2840143	0.87[EUR][1000 genomes]
rs35295338	0.81[EUR][1000 genomes]
rs3772127	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4676684	0.86[EUR][1000 genomes]
rs4676685	0.87[EUR][1000 genomes]
rs4676686	0.86[EUR][1000 genomes]
rs6438645	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6791896	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6792659	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6794341	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6802033	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6803839	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6807711	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7375038	0.87[EUR][1000 genomes]
rs7429247	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7430165	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7611913	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7620842	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7646585	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9289172	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9289173	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9809114	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9812411	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9829053	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9832267	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9835182	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9854052	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9861992	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9864907	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9876021	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[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	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6794677	HCLS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:121396800-121435600	Weak transcription	Psoas Muscle	Psoas
3	chr3:121399000-121425400	Weak transcription	Pancreas	Pancrea
4	chr3:121399000-121426400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:121399000-121440400	Weak transcription	K562	blood
6	chr3:121401200-121429400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:121401200-121434000	Weak transcription	Gastric	stomach
8	chr3:121404000-121432800	Weak transcription	Brain Angular Gyrus	brain
9	chr3:121407400-121429400	Weak transcription	Esophagus	oesophagus
10	chr3:121408200-121428400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:121408600-121424600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:121408600-121424800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:121408600-121424800	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr3:121408600-121427400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:121408600-121428200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr3:121408800-121424800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:121410400-121435600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:121410800-121424400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:121411000-121432000	Weak transcription	NHEK	skin
20	chr3:121411000-121432800	Weak transcription	Fetal Brain Male	brain
21	chr3:121411000-121442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:121411400-121432800	Weak transcription	Colonic Mucosa	Colon
23	chr3:121411400-121437200	Weak transcription	Small Intestine	intestine
24	chr3:121413400-121446200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:121414200-121428000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:121414800-121436200	Weak transcription	Stomach Mucosa	stomach
27	chr3:121415400-121424800	Strong transcription	Liver	Liver
28	chr3:121415400-121427400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:121415600-121428400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:121416000-121425000	Strong transcription	Primary hematopoietic stem cells	blood
31	chr3:121416400-121425200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:121417200-121424200	Weak transcription	Right Ventricle	heart
33	chr3:121417200-121430800	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:121417200-121435800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:121417400-121426200	Weak transcription	Thymus	Thymus
36	chr3:121417400-121431600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:121417600-121424200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:121417600-121425400	Weak transcription	Lung	lung
39	chr3:121417600-121430800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:121417600-121431600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:121417600-121432000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:121417600-121432000	Weak transcription	Fetal Brain Female	brain
43	chr3:121417600-121432800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:121417600-121432800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:121417600-121434200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:121417600-121434200	Weak transcription	Aorta	Aorta
47	chr3:121417600-121435200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:121417600-121437200	Weak transcription	Spleen	Spleen
49	chr3:121417800-121431600	Weak transcription	HSMMtube	muscle
50	chr3:121418000-121432000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links