Variant report

Variant	rs10916268
Chromosome Location	chr1:228334277-228334278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228332924-228334939	K562	blood:	n/a	n/a
2	POLR2A	chr1:228332644-228338827	K562	blood:	n/a	n/a
3	POLR2A	chr1:228334201-228334395	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:228333073-228335536	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:228334176-228335329	K562	blood:	n/a	n/a
6	POLR2A	chr1:228333961-228335173	HepG2	liver:	n/a	n/a
7	GATA1	chr1:228333242-228334942	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228289389..228292049-chr1:228333496..228335357,2	K562	blood:
2	chr1:228289424..228292369-chr1:228333748..228336393,2	MCF-7	breast:
3	chr1:228284520..228292111-chr1:228324853..228335412,14	K562	blood:

No data

Variant related genes	Relation type
GJC2	TF binding region
GUK1	TF binding region
ENSG00000264944	Chromatin interaction
ENSG00000143793	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1059778	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10753445	0.92[CEU][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs10799468	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10799469	0.84[EUR][1000 genomes]
rs10799471	0.83[EUR][1000 genomes]
rs10916265	0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10916271	0.95[EUR][1000 genomes]
rs11584385	0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11799681	0.83[EUR][1000 genomes]
rs11804508	0.85[EUR][1000 genomes]
rs12024649	0.84[EUR][1000 genomes]
rs12084338	0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs12118872	0.82[CEU][hapmap]
rs12130630	0.83[EUR][1000 genomes]
rs12134624	0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs12564763	0.94[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12726781	0.85[EUR][1000 genomes]
rs12745416	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs1331303	0.80[EUR][1000 genomes]
rs1411910	0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs1620111	0.92[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs1629290	0.80[EUR][1000 genomes]
rs1629294	0.92[CEU][hapmap];0.88[GIH][hapmap];0.81[LWK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1745417	0.86[CHB][hapmap]
rs1745423	0.87[TSI][hapmap]
rs1757129	0.81[EUR][1000 genomes]
rs1757132	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1757133	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1757139	0.92[CEU][hapmap];0.83[LWK][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs1757140	0.81[EUR][1000 genomes]
rs1757141	0.81[EUR][1000 genomes]
rs1757144	0.81[EUR][1000 genomes]
rs1757145	0.82[EUR][1000 genomes]
rs1757147	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1757148	0.82[EUR][1000 genomes]
rs1757149	0.92[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1757150	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1757151	0.82[EUR][1000 genomes]
rs1757152	0.83[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.80[LWK][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs1757155	0.81[EUR][1000 genomes]
rs1757156	0.83[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1757158	0.82[EUR][1000 genomes]
rs17640616	0.87[TSI][hapmap]
rs1771459	0.92[CEU][hapmap];0.80[GIH][hapmap];0.81[EUR][1000 genomes]
rs1771460	0.83[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.83[LWK][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs1771461	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771462	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771467	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771469	0.81[EUR][1000 genomes]
rs1771470	0.80[EUR][1000 genomes]
rs1771471	0.81[EUR][1000 genomes]
rs1771472	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771474	0.83[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.81[LWK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1771476	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1771477	0.81[EUR][1000 genomes]
rs1771478	0.81[EUR][1000 genomes]
rs1771479	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771482	0.83[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs1771483	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771484	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs1771485	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1771487	0.88[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs2066237	0.94[ASW][hapmap];0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs2185544	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2298014	0.82[EUR][1000 genomes]
rs2313601	0.91[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs2313602	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776845	0.81[EUR][1000 genomes]
rs2776853	0.84[EUR][1000 genomes]
rs2776855	0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2776856	0.83[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.83[LWK][hapmap];0.88[TSI][hapmap]
rs2792984	0.82[EUR][1000 genomes]
rs2872538	0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs3094912	0.85[CHB][hapmap]
rs3094913	0.86[CHB][hapmap]
rs3094914	0.86[CHB][hapmap]
rs3121191	0.83[EUR][1000 genomes]
rs3121192	0.84[EUR][1000 genomes]
rs3795777	0.80[EUR][1000 genomes]
rs3795782	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs4653536	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653543	0.80[EUR][1000 genomes]
rs4653907	0.81[EUR][1000 genomes]
rs4653915	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653917	0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs4653919	0.81[EUR][1000 genomes]
rs4653920	0.81[EUR][1000 genomes]
rs4653921	0.81[EUR][1000 genomes]
rs4653931	0.81[EUR][1000 genomes]
rs493945	0.91[CEU][hapmap];0.85[TSI][hapmap]
rs55873533	0.83[EUR][1000 genomes]
rs55971985	0.85[EUR][1000 genomes]
rs56112646	0.81[EUR][1000 genomes]
rs61827540	0.81[EUR][1000 genomes]
rs6673893	0.81[EUR][1000 genomes]
rs6682260	0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs708111	0.80[CHB][hapmap]
rs708112	0.82[CHB][hapmap]
rs708114	0.82[CHB][hapmap]
rs72757811	0.83[EUR][1000 genomes]
rs72757812	0.81[EUR][1000 genomes]
rs7512209	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532924	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs7537636	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539762	0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs849749	0.85[TSI][hapmap]
rs947087	0.92[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs964941	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
10	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
11	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
13	nsv549290	chr1:228333652-228349806	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv873258	chr1:228334088-228359775	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
15	nsv873259	chr1:228334277-228359775	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
16	nsv873260	chr1:228334277-228371098	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10916268	OBSCN	cis	Esophagus Mucosa	GTEx
rs10916268	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs10916268	IBA57	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228329000-228336800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:228329000-228339400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:228329000-228339600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:228329200-228337400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:228329400-228336600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:228329400-228337600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:228329400-228337600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:228329400-228338200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:228329600-228335200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:228329600-228335600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:228329600-228336800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:228329800-228336400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:228329800-228336600	Weak transcription	A549	lung
14	chr1:228330000-228334800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:228330000-228335800	Weak transcription	Fetal Lung	lung
16	chr1:228330000-228337200	Genic enhancers	Fetal Muscle Leg	muscle
17	chr1:228330000-228337800	Genic enhancers	Lung	lung
18	chr1:228330200-228336200	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:228330600-228337200	Genic enhancers	Fetal Muscle Trunk	muscle
20	chr1:228331000-228335600	Weak transcription	HUVEC	blood vessel
21	chr1:228331000-228335800	Strong transcription	Fetal Stomach	stomach
22	chr1:228331000-228338800	Weak transcription	HSMMtube	muscle
23	chr1:228331200-228336000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:228331400-228341800	Weak transcription	Psoas Muscle	Psoas
25	chr1:228331600-228337000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:228331600-228337000	Weak transcription	NH-A	brain
27	chr1:228331600-228341000	Genic enhancers	Fetal Thymus	thymus
28	chr1:228331800-228335800	Weak transcription	Brain Substantia Nigra	brain
29	chr1:228331800-228336400	Weak transcription	NHDF-Ad	bronchial
30	chr1:228331800-228336600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:228331800-228336800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:228332000-228334600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:228332000-228335800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:228332000-228336200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:228332000-228336400	Weak transcription	Hela-S3	cervix
36	chr1:228332000-228336400	Weak transcription	HSMM	muscle
37	chr1:228332000-228336600	Weak transcription	Fetal Heart	heart
38	chr1:228332000-228337000	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr1:228332200-228334400	Weak transcription	HMEC	breast
40	chr1:228332200-228334800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:228332200-228334800	Weak transcription	Brain Angular Gyrus	brain
42	chr1:228332200-228335600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:228332200-228335800	Weak transcription	Right Atrium	heart
44	chr1:228332200-228336000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:228332200-228336200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:228332200-228337400	Strong transcription	Dnd41	blood
47	chr1:228332400-228336400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:228332400-228337200	Genic enhancers	Esophagus	oesophagus
49	chr1:228332400-228339400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:228332600-228335800	Weak transcription	Stomach Mucosa	stomach

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