Variant report

Variant	rs1411913
Chromosome Location	chr1:228434746-228434747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228426358..228429102-chr1:228433065..228434825,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10799471	0.82[EUR][1000 genomes]
rs11584385	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11799681	0.81[EUR][1000 genomes]
rs11804508	0.83[EUR][1000 genomes]
rs12024649	0.82[EUR][1000 genomes]
rs12726781	0.83[EUR][1000 genomes]
rs12745416	0.83[EUR][1000 genomes]
rs1331303	0.86[EUR][1000 genomes]
rs1411910	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1620111	0.83[EUR][1000 genomes]
rs1629290	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1629294	0.84[EUR][1000 genomes]
rs1757129	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757132	0.85[EUR][1000 genomes]
rs1757133	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757138	0.84[EUR][1000 genomes]
rs1757139	0.86[EUR][1000 genomes]
rs1757140	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757141	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757142	0.83[EUR][1000 genomes]
rs1757144	0.85[EUR][1000 genomes]
rs1757145	0.86[EUR][1000 genomes]
rs1757147	0.84[EUR][1000 genomes]
rs1757148	0.84[EUR][1000 genomes]
rs1757149	0.85[EUR][1000 genomes]
rs1757150	0.85[EUR][1000 genomes]
rs1757151	0.86[EUR][1000 genomes]
rs1757152	0.84[EUR][1000 genomes]
rs1757153	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1757155	0.85[EUR][1000 genomes]
rs1757156	0.85[EUR][1000 genomes]
rs1757158	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1771459	0.85[EUR][1000 genomes]
rs1771460	0.85[EUR][1000 genomes]
rs1771461	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1771462	0.85[EUR][1000 genomes]
rs1771467	0.85[EUR][1000 genomes]
rs1771468	0.86[EUR][1000 genomes]
rs1771469	0.85[EUR][1000 genomes]
rs1771470	0.86[EUR][1000 genomes]
rs1771471	0.84[EUR][1000 genomes]
rs1771472	0.84[EUR][1000 genomes]
rs1771474	0.84[EUR][1000 genomes]
rs1771476	0.84[EUR][1000 genomes]
rs1771477	0.85[EUR][1000 genomes]
rs1771478	0.85[EUR][1000 genomes]
rs1771479	0.85[EUR][1000 genomes]
rs1771482	0.85[EUR][1000 genomes]
rs1771483	0.85[EUR][1000 genomes]
rs1771484	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1771485	0.84[EUR][1000 genomes]
rs1771487	0.81[EUR][1000 genomes]
rs1934882	1.00[CHB][hapmap]
rs2313601	0.83[EUR][1000 genomes]
rs2776845	0.85[EUR][1000 genomes]
rs2776853	0.83[EUR][1000 genomes]
rs2776855	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2776856	0.85[EUR][1000 genomes]
rs2792984	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2872538	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3121192	0.81[EUR][1000 genomes]
rs3754358	1.00[CHB][hapmap]
rs3795777	0.83[EUR][1000 genomes]
rs4653543	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653545	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653931	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653933	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs489926	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs491293	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs512406	0.82[EUR][1000 genomes]
rs545313	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs546967	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55971985	0.83[EUR][1000 genomes]
rs56112646	0.85[EUR][1000 genomes]
rs566640	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61827540	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7525075	0.83[EUR][1000 genomes]
rs947087	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
9	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
10	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
11	nsv873264	chr1:228423647-228543800	Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv520340	chr1:228423936-228456147	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv873265	chr1:228434395-228525008	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv873266	chr1:228434395-228537942	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv873267	chr1:228434395-228585837	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1411913	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228418400-228436000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:228422200-228434800	ZNF genes & repeats	Dnd41	blood
3	chr1:228426000-228435200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr1:228427000-228435600	ZNF genes & repeats	Brain Germinal Matrix	brain
5	chr1:228428200-228435000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr1:228428400-228435200	ZNF genes & repeats	Primary T cells from cord blood	blood
7	chr1:228428400-228436600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr1:228428600-228434800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
9	chr1:228428600-228435000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
10	chr1:228428600-228435000	ZNF genes & repeats	Fetal Muscle Leg	muscle
11	chr1:228428800-228434800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
12	chr1:228429000-228434800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
13	chr1:228429000-228439400	Strong transcription	HSMMtube	muscle
14	chr1:228430000-228435200	ZNF genes & repeats	Fetal Kidney	kidney
15	chr1:228430200-228435000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:228430400-228434800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
17	chr1:228430400-228434800	ZNF genes & repeats	Fetal Stomach	stomach
18	chr1:228430400-228435000	ZNF genes & repeats	A549	lung
19	chr1:228430400-228435200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:228430400-228435200	ZNF genes & repeats	Thymus	Thymus
21	chr1:228430400-228435800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:228430400-228436600	ZNF genes & repeats	Fetal Intestine Small	intestine
23	chr1:228430600-228447000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:228430800-228434800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:228430800-228435000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:228430800-228435000	ZNF genes & repeats	Esophagus	oesophagus
27	chr1:228430800-228435400	ZNF genes & repeats	Fetal Brain Female	brain
28	chr1:228430800-228440000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:228431000-228435400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:228431000-228436000	Strong transcription	Right Ventricle	heart
31	chr1:228431200-228439800	Strong transcription	Left Ventricle	heart
32	chr1:228431400-228436000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:228432000-228434800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
34	chr1:228432000-228435200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
35	chr1:228432000-228436800	Strong transcription	Psoas Muscle	Psoas
36	chr1:228432200-228434800	Strong transcription	Ovary	ovary
37	chr1:228432200-228435200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:228432200-228435400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:228432200-228435800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:228432600-228435200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:228432600-228435800	Strong transcription	Fetal Heart	heart
42	chr1:228432800-228435000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
43	chr1:228433000-228435000	Strong transcription	Fetal Brain Male	brain
44	chr1:228433200-228434800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:228433200-228442400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:228433400-228435000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr1:228433400-228435200	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr1:228433400-228436400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:228433400-228449400	Weak transcription	Brain Anterior Caudate	brain
50	chr1:228433600-228438000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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