Variant report

Variant	rs1771485
Chromosome Location	chr1:228406675-228406676
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228405795..228408682-chr1:228408698..228410594,4	K562	blood:
2	chr1:228399642..228402754-chr1:228404803..228408505,4	MCF-7	breast:
3	chr1:228390548..228393233-chr1:228405231..228408783,3	K562	blood:
4	chr1:228343198..228344704-chr1:228404539..228407474,2	MCF-7	breast:
5	chr1:228404999..228407013-chr1:228410390..228412165,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162913	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10158357	0.84[CEU][hapmap]
rs1059778	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs10753445	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10799468	0.82[EUR][1000 genomes]
rs10799471	0.94[EUR][1000 genomes]
rs10916265	0.84[CEU][hapmap]
rs10916268	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10916271	0.85[EUR][1000 genomes]
rs11580411	0.84[EUR][1000 genomes]
rs11584385	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11799681	0.94[EUR][1000 genomes]
rs11804508	0.96[EUR][1000 genomes]
rs12024649	0.95[EUR][1000 genomes]
rs12084338	0.84[CEU][hapmap]
rs12118872	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs12130630	0.85[CEU][hapmap]
rs12564763	0.88[CEU][hapmap]
rs12726781	0.96[EUR][1000 genomes]
rs12745416	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1331303	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1411910	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1411911	0.84[EUR][1000 genomes]
rs1411913	0.84[EUR][1000 genomes]
rs1557026	0.85[CEU][hapmap]
rs1620111	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1629290	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1629294	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1757129	0.96[EUR][1000 genomes]
rs1757132	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757133	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1757138	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757139	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757140	0.97[EUR][1000 genomes]
rs1757141	0.97[EUR][1000 genomes]
rs1757142	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1757144	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757145	0.98[EUR][1000 genomes]
rs1757147	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757148	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757149	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757150	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757151	0.97[EUR][1000 genomes]
rs1757152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757155	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757156	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757158	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17640616	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs1771459	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771460	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1771461	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs1771462	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1771467	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771468	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1771469	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1771470	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1771471	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771472	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771476	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771477	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771478	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771479	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771483	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771484	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs1771487	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2066237	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2185544	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2313601	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2313602	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2776845	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776853	0.96[EUR][1000 genomes]
rs2776855	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2776856	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2792984	0.96[EUR][1000 genomes]
rs2872538	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2989563	0.87[EUR][1000 genomes]
rs3121188	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3121190	0.87[EUR][1000 genomes]
rs3121191	0.92[EUR][1000 genomes]
rs3121192	0.94[EUR][1000 genomes]
rs3795777	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3795782	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs4653536	0.83[EUR][1000 genomes]
rs4653543	0.96[EUR][1000 genomes]
rs4653545	0.92[EUR][1000 genomes]
rs4653915	0.88[CEU][hapmap]
rs4653917	0.84[CEU][hapmap]
rs4653921	0.85[CEU][hapmap]
rs4653931	0.97[EUR][1000 genomes]
rs4653933	0.94[EUR][1000 genomes]
rs4653934	0.84[EUR][1000 genomes]
rs489926	0.90[EUR][1000 genomes]
rs491293	0.91[EUR][1000 genomes]
rs493945	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs512406	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs545313	0.92[EUR][1000 genomes]
rs546967	0.92[EUR][1000 genomes]
rs55658545	0.85[EUR][1000 genomes]
rs55971985	0.96[EUR][1000 genomes]
rs56112646	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56168609	0.82[EUR][1000 genomes]
rs566640	0.92[EUR][1000 genomes]
rs61825279	0.81[EUR][1000 genomes]
rs61827540	0.97[EUR][1000 genomes]
rs6426492	0.80[CEU][hapmap]
rs6657968	0.85[CEU][hapmap]
rs6661539	0.86[EUR][1000 genomes]
rs6673893	0.85[CEU][hapmap]
rs6682260	0.84[CEU][hapmap]
rs72757829	0.84[EUR][1000 genomes]
rs7512209	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs7525075	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7532141	0.83[EUR][1000 genomes]
rs7532924	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7537636	1.00[CEU][hapmap]
rs7539762	0.84[CEU][hapmap]
rs947087	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[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
rs1771485	OBSCN	cis	Esophagus Mucosa	GTEx
rs1771485	IBA57	cis	Whole Blood	GTEx
rs1771485	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	chr1:228401400-228412200	Weak transcription	HSMMtube	muscle
2	chr1:228401400-228412600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:228401600-228412200	Weak transcription	Right Atrium	heart
4	chr1:228401800-228407200	Weak transcription	Ovary	ovary
5	chr1:228401800-228412000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:228402000-228406800	Weak transcription	Psoas Muscle	Psoas
7	chr1:228402000-228407200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:228402000-228407200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:228402000-228412000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:228402000-228412200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:228402000-228412200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:228402000-228412600	Weak transcription	Fetal Kidney	kidney
13	chr1:228402200-228410200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:228402200-228411800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:228402200-228412200	Weak transcription	A549	lung
16	chr1:228402200-228412200	Weak transcription	Hela-S3	cervix
17	chr1:228402200-228412200	Weak transcription	NHEK	skin
18	chr1:228402200-228412400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:228402200-228412600	Weak transcription	Primary B cells from cord blood	blood
20	chr1:228402200-228415200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:228402200-228425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:228402200-228428800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:228402400-228408400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:228402400-228411400	Strong transcription	Fetal Intestine Small	intestine
25	chr1:228402400-228411600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:228402400-228412400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:228402400-228412600	Weak transcription	HMEC	breast
28	chr1:228402600-228408400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:228402600-228408400	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr1:228402600-228408600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:228402600-228409000	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr1:228402600-228410600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:228402600-228418000	Strong transcription	Primary T cells from cord blood	blood
34	chr1:228402800-228407200	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr1:228402800-228408200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:228402800-228408400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:228402800-228408800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:228402800-228409000	Strong transcription	Thymus	Thymus
39	chr1:228402800-228410400	Weak transcription	Fetal Lung	lung
40	chr1:228402800-228411800	Weak transcription	Esophagus	oesophagus
41	chr1:228402800-228412600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:228403000-228410200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:228403000-228412200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:228403000-228412200	Weak transcription	Colonic Mucosa	Colon
45	chr1:228403000-228428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:228403200-228418000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:228403400-228408000	Strong transcription	Fetal Intestine Large	intestine
48	chr1:228403400-228408400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:228403400-228408400	Strong transcription	Fetal Brain Female	brain
50	chr1:228403400-228408600	Strong transcription	H9 Cell Line	embryonic stem cell

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