Variant report

Variant	rs3795777
Chromosome Location	chr1:228404668-228404669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228330921..228333464-chr1:228403615..228405711,2	MCF-7	breast:
2	chr1:228343198..228344704-chr1:228404539..228407474,2	MCF-7	breast:
3	chr1:228403882..228405621-chr1:228418994..228420912,2	K562	blood:
4	chr1:228401876..228404808-chr1:228460949..228463356,3	K562	blood:

Variant related genes	Relation type
ENSG00000269890	Chromatin interaction
ENSG00000143774	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1059778	0.83[EUR][1000 genomes]
rs10753445	0.83[EUR][1000 genomes]
rs10799471	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916268	0.80[EUR][1000 genomes]
rs10916271	0.83[EUR][1000 genomes]
rs11580411	0.83[EUR][1000 genomes]
rs11584385	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11799681	0.92[EUR][1000 genomes]
rs11804508	0.94[EUR][1000 genomes]
rs12024649	0.93[EUR][1000 genomes]
rs12118872	0.81[EUR][1000 genomes]
rs12726781	0.94[EUR][1000 genomes]
rs12745416	0.94[EUR][1000 genomes]
rs1331303	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1411910	0.95[EUR][1000 genomes]
rs1411911	0.83[EUR][1000 genomes]
rs1411913	0.83[EUR][1000 genomes]
rs1620111	0.94[EUR][1000 genomes]
rs1629290	0.94[EUR][1000 genomes]
rs1629294	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1757129	0.95[EUR][1000 genomes]
rs1757132	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757133	0.94[EUR][1000 genomes]
rs1757138	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757139	0.97[EUR][1000 genomes]
rs1757140	0.94[EUR][1000 genomes]
rs1757141	0.94[EUR][1000 genomes]
rs1757142	0.92[EUR][1000 genomes]
rs1757144	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1757145	0.96[EUR][1000 genomes]
rs1757147	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1757148	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1757149	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1757150	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1757151	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1757152	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1757155	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1757156	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1757158	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17640616	0.84[EUR][1000 genomes]
rs1771459	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1771460	0.96[EUR][1000 genomes]
rs1771461	0.95[EUR][1000 genomes]
rs1771462	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1771467	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1771468	0.94[EUR][1000 genomes]
rs1771469	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1771470	0.96[EUR][1000 genomes]
rs1771471	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771472	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771474	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771476	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1771477	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1771478	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771479	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1771482	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771483	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771484	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1771485	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771487	0.91[EUR][1000 genomes]
rs2185544	0.83[EUR][1000 genomes]
rs2313601	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2313602	0.80[EUR][1000 genomes]
rs2776845	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2776853	0.93[EUR][1000 genomes]
rs2776855	0.94[EUR][1000 genomes]
rs2776856	0.96[EUR][1000 genomes]
rs2792984	0.93[EUR][1000 genomes]
rs2872538	0.95[EUR][1000 genomes]
rs2989563	0.87[EUR][1000 genomes]
rs3121188	0.86[EUR][1000 genomes]
rs3121190	0.87[EUR][1000 genomes]
rs3121191	0.92[EUR][1000 genomes]
rs3121192	0.94[EUR][1000 genomes]
rs3795782	0.82[EUR][1000 genomes]
rs4653536	0.81[EUR][1000 genomes]
rs4653543	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653545	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4653931	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653933	0.92[EUR][1000 genomes]
rs4653934	0.82[EUR][1000 genomes]
rs489926	0.88[EUR][1000 genomes]
rs491293	0.90[EUR][1000 genomes]
rs493945	0.80[EUR][1000 genomes]
rs512406	0.90[EUR][1000 genomes]
rs545313	0.90[EUR][1000 genomes]
rs546967	0.90[EUR][1000 genomes]
rs55658545	0.84[EUR][1000 genomes]
rs55971985	0.94[EUR][1000 genomes]
rs56112646	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs566640	0.91[EUR][1000 genomes]
rs61827540	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6661539	0.86[EUR][1000 genomes]
rs72757829	0.83[EUR][1000 genomes]
rs7525075	0.91[EUR][1000 genomes]
rs7532141	0.81[EUR][1000 genomes]
rs7532924	0.86[EUR][1000 genomes]
rs947087	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3795777	IBA57	cis	Whole Blood	GTEx
rs3795777	OBSCN	cis	Esophagus Mucosa	GTEx
rs3795777	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228395800-228405200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr1:228401400-228405200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:228401400-228412200	Weak transcription	HSMMtube	muscle
4	chr1:228401400-228412600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:228401600-228412200	Weak transcription	Right Atrium	heart
6	chr1:228401800-228407200	Weak transcription	Ovary	ovary
7	chr1:228401800-228412000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:228402000-228405000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
9	chr1:228402000-228406800	Weak transcription	Psoas Muscle	Psoas
10	chr1:228402000-228407200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:228402000-228407200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:228402000-228412000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:228402000-228412200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:228402000-228412200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:228402000-228412600	Weak transcription	Fetal Kidney	kidney
16	chr1:228402200-228406600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:228402200-228410200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:228402200-228411800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:228402200-228412200	Weak transcription	A549	lung
20	chr1:228402200-228412200	Weak transcription	Hela-S3	cervix
21	chr1:228402200-228412200	Weak transcription	NHEK	skin
22	chr1:228402200-228412400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:228402200-228412600	Weak transcription	Primary B cells from cord blood	blood
24	chr1:228402200-228415200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:228402200-228425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:228402200-228428800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:228402400-228404800	Genic enhancers	Fetal Muscle Leg	muscle
28	chr1:228402400-228406600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:228402400-228408400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:228402400-228411400	Strong transcription	Fetal Intestine Small	intestine
31	chr1:228402400-228411600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:228402400-228412400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:228402400-228412600	Weak transcription	HMEC	breast
34	chr1:228402600-228406200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:228402600-228408400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:228402600-228408400	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr1:228402600-228408600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:228402600-228409000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr1:228402600-228410600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:228402600-228418000	Strong transcription	Primary T cells from cord blood	blood
41	chr1:228402800-228407200	Genic enhancers	Fetal Muscle Trunk	muscle
42	chr1:228402800-228408200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:228402800-228408400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:228402800-228408800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:228402800-228409000	Strong transcription	Thymus	Thymus
46	chr1:228402800-228410400	Weak transcription	Fetal Lung	lung
47	chr1:228402800-228411800	Weak transcription	Esophagus	oesophagus
48	chr1:228402800-228412600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:228403000-228410200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:228403000-228412200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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