Variant report

Variant	rs55658545
Chromosome Location	chr1:228411324-228411325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228407306..228411999-chr1:228412295..228415050,4	K562	blood:
2	chr1:228407306..228411999-chr1:228412295..228416286,6	K562	blood:
3	chr1:228404999..228407013-chr1:228410390..228412165,2	MCF-7	breast:

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10799471	0.83[EUR][1000 genomes]
rs10916277	0.86[EUR][1000 genomes]
rs11584385	0.86[EUR][1000 genomes]
rs11799681	0.83[EUR][1000 genomes]
rs11804508	0.84[EUR][1000 genomes]
rs12024649	0.83[EUR][1000 genomes]
rs12084338	0.86[EUR][1000 genomes]
rs12097591	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12130630	0.85[EUR][1000 genomes]
rs12134624	0.82[EUR][1000 genomes]
rs12726781	0.84[EUR][1000 genomes]
rs12745416	0.84[EUR][1000 genomes]
rs1331303	0.85[EUR][1000 genomes]
rs1411910	0.86[EUR][1000 genomes]
rs1411911	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557026	0.90[EUR][1000 genomes]
rs1620111	0.84[EUR][1000 genomes]
rs1629290	0.86[EUR][1000 genomes]
rs1629294	0.85[EUR][1000 genomes]
rs1757129	0.86[EUR][1000 genomes]
rs1757132	0.84[EUR][1000 genomes]
rs1757133	0.86[EUR][1000 genomes]
rs1757138	0.83[EUR][1000 genomes]
rs1757139	0.85[EUR][1000 genomes]
rs1757140	0.86[EUR][1000 genomes]
rs1757141	0.86[EUR][1000 genomes]
rs1757142	0.80[EUR][1000 genomes]
rs1757144	0.84[EUR][1000 genomes]
rs1757145	0.87[EUR][1000 genomes]
rs1757147	0.85[EUR][1000 genomes]
rs1757148	0.85[EUR][1000 genomes]
rs1757149	0.86[EUR][1000 genomes]
rs1757150	0.86[EUR][1000 genomes]
rs1757151	0.87[EUR][1000 genomes]
rs1757152	0.85[EUR][1000 genomes]
rs1757155	0.86[EUR][1000 genomes]
rs1757156	0.86[EUR][1000 genomes]
rs1757158	0.87[EUR][1000 genomes]
rs17623766	0.89[EUR][1000 genomes]
rs17640616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771459	0.84[EUR][1000 genomes]
rs1771460	0.84[EUR][1000 genomes]
rs1771461	0.86[EUR][1000 genomes]
rs1771462	0.84[EUR][1000 genomes]
rs1771467	0.84[EUR][1000 genomes]
rs1771468	0.83[EUR][1000 genomes]
rs1771469	0.84[EUR][1000 genomes]
rs1771470	0.84[EUR][1000 genomes]
rs1771471	0.84[EUR][1000 genomes]
rs1771472	0.85[EUR][1000 genomes]
rs1771474	0.85[EUR][1000 genomes]
rs1771476	0.85[EUR][1000 genomes]
rs1771477	0.86[EUR][1000 genomes]
rs1771478	0.86[EUR][1000 genomes]
rs1771479	0.86[EUR][1000 genomes]
rs1771482	0.86[EUR][1000 genomes]
rs1771483	0.86[EUR][1000 genomes]
rs1771484	0.87[EUR][1000 genomes]
rs1771485	0.85[EUR][1000 genomes]
rs1771487	0.82[EUR][1000 genomes]
rs2298014	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2313600	0.89[EUR][1000 genomes]
rs2313601	0.84[EUR][1000 genomes]
rs2776845	0.85[EUR][1000 genomes]
rs2776853	0.84[EUR][1000 genomes]
rs2776855	0.85[EUR][1000 genomes]
rs2776856	0.84[EUR][1000 genomes]
rs2792984	0.85[EUR][1000 genomes]
rs2872538	0.86[EUR][1000 genomes]
rs3121191	0.80[EUR][1000 genomes]
rs3121192	0.82[EUR][1000 genomes]
rs3795777	0.84[EUR][1000 genomes]
rs41303079	0.86[EUR][1000 genomes]
rs4653543	0.85[EUR][1000 genomes]
rs4653545	0.83[EUR][1000 genomes]
rs4653907	0.84[EUR][1000 genomes]
rs4653917	0.85[EUR][1000 genomes]
rs4653919	0.85[EUR][1000 genomes]
rs4653920	0.86[EUR][1000 genomes]
rs4653921	0.87[EUR][1000 genomes]
rs4653931	0.86[EUR][1000 genomes]
rs4653933	0.85[EUR][1000 genomes]
rs489926	0.82[EUR][1000 genomes]
rs491293	0.83[EUR][1000 genomes]
rs512406	0.83[EUR][1000 genomes]
rs545313	0.83[EUR][1000 genomes]
rs546967	0.83[EUR][1000 genomes]
rs55873533	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs55971985	0.84[EUR][1000 genomes]
rs56112646	0.84[EUR][1000 genomes]
rs566640	0.83[EUR][1000 genomes]
rs61825279	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827540	0.86[EUR][1000 genomes]
rs6657968	0.90[EUR][1000 genomes]
rs6661539	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6673893	0.87[EUR][1000 genomes]
rs6682260	0.85[EUR][1000 genomes]
rs72757811	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72757812	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72757824	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72757827	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72757829	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7525075	0.83[EUR][1000 genomes]
rs7532141	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7539762	0.87[EUR][1000 genomes]
rs947087	0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55658545	OBSCN	cis	Esophagus Mucosa	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	chr1:228401800-228412000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:228402000-228412000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:228402000-228412200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:228402000-228412200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:228402000-228412600	Weak transcription	Fetal Kidney	kidney
9	chr1:228402200-228411800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:228402200-228412200	Weak transcription	A549	lung
11	chr1:228402200-228412200	Weak transcription	Hela-S3	cervix
12	chr1:228402200-228412200	Weak transcription	NHEK	skin
13	chr1:228402200-228412400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:228402200-228412600	Weak transcription	Primary B cells from cord blood	blood
15	chr1:228402200-228415200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:228402200-228425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:228402200-228428800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:228402400-228411400	Strong transcription	Fetal Intestine Small	intestine
19	chr1:228402400-228411600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:228402400-228412400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:228402400-228412600	Weak transcription	HMEC	breast
22	chr1:228402600-228418000	Strong transcription	Primary T cells from cord blood	blood
23	chr1:228402800-228411800	Weak transcription	Esophagus	oesophagus
24	chr1:228402800-228412600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:228403000-228412200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:228403000-228412200	Weak transcription	Colonic Mucosa	Colon
27	chr1:228403000-228428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:228403200-228418000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:228403400-228415000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:228404200-228411600	Strong transcription	Fetal Stomach	stomach
31	chr1:228404200-228412000	Weak transcription	Brain Anterior Caudate	brain
32	chr1:228404200-228412200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:228404200-228412600	Weak transcription	Fetal Brain Male	brain
34	chr1:228404400-228411800	Weak transcription	Pancreas	Pancrea
35	chr1:228404800-228412000	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:228407600-228411800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:228407600-228412200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:228407600-228412200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:228408000-228411800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:228408000-228411800	Weak transcription	Fetal Intestine Large	intestine
41	chr1:228408000-228412200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:228408200-228411800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:228408200-228411800	Weak transcription	Fetal Thymus	thymus
44	chr1:228408200-228411800	Weak transcription	Ovary	ovary
45	chr1:228408200-228412000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:228408200-228412200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:228408200-228412200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:228408200-228412200	Weak transcription	Psoas Muscle	Psoas
49	chr1:228408400-228411600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:228408400-228411800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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