Variant report

Variant	rs1771479
Chromosome Location	chr1:228412953-228412954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228412002..228414034-chr1:228460124..228463067,2	K562	blood:
2	chr1:228407306..228411999-chr1:228412295..228416286,6	K562	blood:
3	chr1:228407306..228411999-chr1:228412295..228415050,4	K562	blood:

Variant related genes	Relation type
ENSG00000269890	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10158357	0.84[CEU][hapmap]
rs1059778	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[EUR][1000 genomes]
rs10753445	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10799468	0.81[EUR][1000 genomes]
rs10799471	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10916265	0.88[CEU][hapmap]
rs10916268	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10916271	0.84[EUR][1000 genomes]
rs11580411	0.85[EUR][1000 genomes]
rs11584385	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11799681	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11804508	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12024649	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12084338	0.84[CEU][hapmap]
rs12118872	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs12130630	0.81[CEU][hapmap]
rs12134624	0.83[CEU][hapmap]
rs12564763	0.88[CEU][hapmap]
rs12726781	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12745416	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1331303	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1411910	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1411911	0.85[EUR][1000 genomes]
rs1411913	0.85[EUR][1000 genomes]
rs1557026	0.81[CEU][hapmap]
rs1620111	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1629290	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1629294	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757129	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1757132	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757133	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1757138	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757139	1.00[CEU][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757140	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1757141	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1757142	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757144	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757145	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1757147	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757148	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757151	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1757152	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757155	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757156	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757158	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17640616	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1771459	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1771460	1.00[CEU][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1771461	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1771462	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1771467	0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1771468	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1771469	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1771470	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1771471	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771472	0.96[CEU][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771474	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771476	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771477	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771478	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771482	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771483	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771484	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1771485	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]
rs1771487	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2066237	1.00[CEU][hapmap];0.80[CHB][hapmap]
rs2185544	0.84[EUR][1000 genomes]
rs2313601	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2313602	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2776845	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2776853	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2776855	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2776856	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2792984	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2872538	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2989563	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3121188	0.85[EUR][1000 genomes]
rs3121190	0.86[EUR][1000 genomes]
rs3121191	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3121192	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3795777	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3795782	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs4653536	0.82[EUR][1000 genomes]
rs4653543	0.96[EUR][1000 genomes]
rs4653545	0.93[EUR][1000 genomes]
rs4653915	0.88[CEU][hapmap]
rs4653917	0.84[CEU][hapmap]
rs4653921	0.81[CEU][hapmap]
rs4653931	0.97[EUR][1000 genomes]
rs4653933	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653934	0.84[EUR][1000 genomes]
rs489926	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs491293	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs493945	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs512406	0.92[EUR][1000 genomes]
rs545313	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs546967	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55658545	0.86[EUR][1000 genomes]
rs55971985	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56112646	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56168609	0.82[EUR][1000 genomes]
rs566640	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61825279	0.82[EUR][1000 genomes]
rs61827540	0.97[EUR][1000 genomes]
rs6426492	0.80[CEU][hapmap]
rs6657968	0.81[CEU][hapmap]
rs6661539	0.86[EUR][1000 genomes]
rs6673893	0.81[CEU][hapmap]
rs6682260	0.84[CEU][hapmap]
rs72757829	0.83[EUR][1000 genomes]
rs7512209	1.00[CEU][hapmap]
rs7525075	0.93[EUR][1000 genomes]
rs7532141	0.83[EUR][1000 genomes]
rs7532924	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7537636	1.00[CEU][hapmap]
rs7539762	0.84[CEU][hapmap]
rs947087	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1771479	IBA57	cis	Whole Blood	GTEx
rs1771479	OBSCN	cis	Esophagus Mucosa	GTEx
rs1771479	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228402200-228415200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:228402200-228425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:228402200-228428800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:228402600-228418000	Strong transcription	Primary T cells from cord blood	blood
5	chr1:228403000-228428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:228403200-228418000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:228403400-228415000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:228410000-228416600	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr1:228410200-228413600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:228410200-228414800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
11	chr1:228410400-228415600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:228410600-228416400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:228410800-228413000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
14	chr1:228410800-228416800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:228411000-228413200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr1:228411000-228415000	Weak transcription	Small Intestine	intestine
17	chr1:228411400-228413400	ZNF genes & repeats	Fetal Intestine Small	intestine
18	chr1:228411400-228413600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:228411600-228413200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
20	chr1:228411600-228413600	ZNF genes & repeats	Fetal Stomach	stomach
21	chr1:228411600-228413800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:228411600-228413800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:228411600-228416000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:228411600-228416800	Strong transcription	Dnd41	blood
25	chr1:228411800-228413000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:228411800-228413000	ZNF genes & repeats	Gastric	stomach
27	chr1:228411800-228413200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:228411800-228413200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr1:228411800-228413200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr1:228411800-228413200	ZNF genes & repeats	Esophagus	oesophagus
31	chr1:228411800-228413200	ZNF genes & repeats	Ovary	ovary
32	chr1:228411800-228413400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
33	chr1:228411800-228413400	ZNF genes & repeats	Brain Germinal Matrix	brain
34	chr1:228411800-228413600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:228411800-228413600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:228411800-228413800	ZNF genes & repeats	Pancreas	Pancrea
37	chr1:228411800-228414200	ZNF genes & repeats	Lung	lung
38	chr1:228411800-228414200	ZNF genes & repeats	Spleen	Spleen
39	chr1:228411800-228415000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:228411800-228416200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:228411800-228416400	Weak transcription	K562	blood
42	chr1:228411800-228417000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:228411800-228420200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:228412000-228413000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:228412000-228413000	ZNF genes & repeats	Thymus	Thymus
46	chr1:228412000-228413200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
47	chr1:228412000-228413200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
48	chr1:228412000-228413400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:228412000-228413600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:228412000-228413600	ZNF genes & repeats	Fetal Muscle Leg	muscle

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