Variant report

Variant	rs3795774
Chromosome Location	chr1:228361128-228361129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228269154..228271874-chr1:228360119..228363775,3	K562	blood:
2	chr1:228320957..228324264-chr1:228357884..228361663,3	MCF-7	breast:
3	chr1:228360767..228363057-chr1:228399837..228402220,2	MCF-7	breast:
4	chr1:228350414..228357594-chr1:228359448..228365919,31	MCF-7	breast:
5	chr1:228295318..228298683-chr1:228360322..228363984,4	K562	blood:
6	chr1:228359729..228361744-chr1:228520707..228523201,2	K562	blood:

Variant related genes	Relation type
ENSG00000162910	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000227625	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000162913	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000154358	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10127705	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1048503	0.82[CHB][hapmap]
rs10495278	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495279	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916266	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1094602	1.00[EUR][1000 genomes]
rs1094603	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11577976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11580599	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11581037	1.00[CEU][hapmap]
rs11581169	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11582369	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11584418	1.00[CEU][hapmap]
rs11584499	0.82[CHB][hapmap]
rs11586055	1.00[CEU][hapmap]
rs12034268	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12039801	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12088423	1.00[CEU][hapmap]
rs1771486	0.85[EUR][1000 genomes]
rs1803695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28587961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34687764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3738680	0.82[CHB][hapmap]
rs3738681	0.82[CHB][hapmap]
rs3795773	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41303083	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653906	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs4653908	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653909	0.90[EUR][1000 genomes]
rs4653914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61825156	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61825157	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61825159	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61827462	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6663726	0.90[EUR][1000 genomes]
rs6668719	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs7530253	1.00[EUR][1000 genomes]
rs7537552	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs9287011	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9970544	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
8	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised 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 miRNA target site	106 gene(s)	inside rSNPs	diseases
9	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
10	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv873260	chr1:228334277-228371098	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
13	nsv873262	chr1:228340653-228371098	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
14	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
15	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
16	esv1806558	chr1:228358977-228365154	Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
17	esv1808523	chr1:228359177-228400358	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	esv3439695	chr1:228360954-228363502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
19	esv3439260	chr1:228361129-228363177	Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228354400-228362600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:228354400-228384600	Weak transcription	Aorta	Aorta
3	chr1:228354600-228361200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:228354600-228362200	Weak transcription	Brain Germinal Matrix	brain
5	chr1:228354600-228362200	Weak transcription	Fetal Thymus	thymus
6	chr1:228354600-228362400	Weak transcription	Psoas Muscle	Psoas
7	chr1:228354600-228363600	Weak transcription	Primary B cells from cord blood	blood
8	chr1:228354600-228370400	Weak transcription	Right Atrium	heart
9	chr1:228354600-228382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:228354600-228385200	Weak transcription	Left Ventricle	heart
11	chr1:228354800-228361200	Weak transcription	Fetal Lung	lung
12	chr1:228354800-228361400	Weak transcription	Esophagus	oesophagus
13	chr1:228354800-228361400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:228354800-228361400	Weak transcription	A549	lung
15	chr1:228354800-228361600	Weak transcription	Colonic Mucosa	Colon
16	chr1:228354800-228362200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:228354800-228362200	Weak transcription	NHLF	lung
18	chr1:228354800-228362400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:228354800-228362400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:228354800-228362400	Weak transcription	Adipose Nuclei	Adipose
21	chr1:228354800-228362400	Weak transcription	Brain Anterior Caudate	brain
22	chr1:228354800-228362400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:228354800-228362400	Weak transcription	Fetal Brain Male	brain
24	chr1:228354800-228362600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:228354800-228362600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:228354800-228362600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:228354800-228362600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:228354800-228362800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:228354800-228362800	Weak transcription	Brain Angular Gyrus	brain
30	chr1:228354800-228362800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:228354800-228362800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:228354800-228363400	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:228354800-228364400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:228354800-228364400	Weak transcription	Brain Substantia Nigra	brain
35	chr1:228354800-228364600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:228354800-228365200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:228354800-228366400	Weak transcription	Liver	Liver
38	chr1:228354800-228367000	Weak transcription	Osteobl	bone
39	chr1:228354800-228370800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:228354800-228371200	Weak transcription	HSMMtube	muscle
41	chr1:228354800-228373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:228355000-228361200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:228355000-228361200	Weak transcription	K562	blood
44	chr1:228355000-228361400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:228355000-228361400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:228355000-228361400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:228355000-228361400	Weak transcription	NHEK	skin
48	chr1:228355000-228362200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:228355000-228362400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:228355000-228362400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links