Variant report

Variant	rs2989563
Chromosome Location	chr1:228401632-228401633
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:228399607-228402252	H1-hESC	embryonic stem cell:	n/a	n/a
2	EGR1	chr1:228401240-228401980	K562	blood:	n/a	chr1:228401631-228401645 chr1:228401596-228401610
3	MAX	chr1:228400625-228402064	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr1:228401030-228401692	K562	blood:	n/a	n/a
5	CREB1	chr1:228400960-228401650	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr1:228401052-228401659	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr1:228401048-228401694	MCF-7	breast:	n/a	n/a
8	CTCF	chr1:228401619-228401688	GM19239	blood:	n/a	n/a
9	CREB1	chr1:228401066-228401635	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr1:228400990-228401688	SK-N-SH	brain:	n/a	n/a
11	MXI1	chr1:228400149-228402453	SK-N-SH	brain:	n/a	n/a
12	CREB1	chr1:228400704-228401652	K562	blood:	n/a	n/a
13	CTCF	chr1:228400930-228401753	SK-N-SH	brain:	n/a	n/a
14	REST	chr1:228400662-228401660	H1-neurons	neurons:	n/a	n/a
15	RAD21	chr1:228401087-228401640	MCF-7	breast:	n/a	n/a
16	MAX	chr1:228400694-228401672	HCT-116	colon:	n/a	n/a
17	E2F6	chr1:228400824-228401637	A549	lung:	n/a	chr1:228401046-228401053 chr1:228401045-228401057 chr1:228401046-228401053 chr1:228401046-228401053
18	POLR2A	chr1:228400679-228402103	ECC-1	luminal epithelium:	n/a	n/a
19	MXI1	chr1:228400727-228402575	IMR90	lung:	n/a	n/a
20	SIN3A	chr1:228399839-228402012	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr1:228400778-228401665	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAZ	chr1:228400621-228401690	K562	blood:	n/a	n/a
23	CREB1	chr1:228401171-228401649	GM12878	blood:	n/a	n/a
24	MAX	chr1:228400662-228401690	A549	lung:	n/a	n/a
25	EGR1	chr1:228401188-228402032	K562	blood:	n/a	chr1:228401631-228401645 chr1:228401596-228401610
26	E2F6	chr1:228400695-228401682	K562	blood:	n/a	chr1:228401046-228401053 chr1:228401045-228401057 chr1:228401046-228401053 chr1:228401046-228401053 chr1:228400708-228400717
27	CTCF	chr1:228400942-228401707	A549	lung:	n/a	n/a
28	MAZ	chr1:228400505-228402251	IMR90	lung:	n/a	n/a
29	HMGN3	chr1:228401164-228402041	K562	blood:	n/a	n/a
30	EGR1	chr1:228401563-228401671	GM12878	blood:	n/a	chr1:228401631-228401645 chr1:228401596-228401610
31	CHD1	chr1:228400776-228401951	IMR90	lung:	n/a	n/a
32	MAX	chr1:228400476-228401850	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228352301..228356055-chr1:228400478..228402839,5	K562	blood:
2	chr1:228400032..228401961-chr1:228675104..228677391,2	MCF-7	breast:
3	chr1:228399534..228402324-chr1:228461653..228463776,2	MCF-7	breast:
4	chr1:228352180..228354320-chr1:228400730..228402843,3	MCF-7	breast:
5	chr1:228270338..228271968-chr1:228400103..228402238,2	MCF-7	breast:
6	chr1:228400118..228403034-chr1:228591844..228593875,2	MCF-7	breast:
7	chr1:228400987..228403639-chr1:228644070..228647036,3	K562	blood:
8	chr1:228401076..228403639-chr1:228645192..228647036,2	K562	blood:
9	chr1:228360767..228363057-chr1:228399837..228402220,2	MCF-7	breast:

Variant related genes	Relation type
C1orf145	TF binding region
OBSCN	TF binding region
ENSG00000168159	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000269890	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000269934	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000203684	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10799471	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11584385	0.87[EUR][1000 genomes]
rs11799681	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11804508	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12024649	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12726781	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12745416	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1331303	0.85[EUR][1000 genomes]
rs1411910	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1620111	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1629290	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1629294	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1757129	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1757132	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1757133	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1757138	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1757139	0.85[EUR][1000 genomes]
rs1757140	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1757141	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1757142	0.84[EUR][1000 genomes]
rs1757144	0.85[EUR][1000 genomes]
rs1757145	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1757147	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1757148	0.86[EUR][1000 genomes]
rs1757149	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1757150	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1757151	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1757152	0.85[EUR][1000 genomes]
rs1757155	0.85[EUR][1000 genomes]
rs1757156	0.86[EUR][1000 genomes]
rs1757158	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1771459	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1771460	0.84[EUR][1000 genomes]
rs1771461	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1771462	0.85[EUR][1000 genomes]
rs1771467	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1771468	0.84[EUR][1000 genomes]
rs1771469	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1771470	0.85[EUR][1000 genomes]
rs1771471	0.85[EUR][1000 genomes]
rs1771472	0.86[EUR][1000 genomes]
rs1771474	0.86[EUR][1000 genomes]
rs1771476	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1771477	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1771478	0.86[EUR][1000 genomes]
rs1771479	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1771482	0.85[EUR][1000 genomes]
rs1771483	0.86[EUR][1000 genomes]
rs1771484	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1771485	0.87[EUR][1000 genomes]
rs1771487	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2313601	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2776845	0.86[EUR][1000 genomes]
rs2776853	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2776855	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2776856	0.84[EUR][1000 genomes]
rs2792984	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2872538	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3121190	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3121191	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3121192	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3795777	0.87[EUR][1000 genomes]
rs4653543	0.86[EUR][1000 genomes]
rs4653545	0.82[EUR][1000 genomes]
rs4653931	0.87[EUR][1000 genomes]
rs4653933	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs489926	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs491293	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs512406	0.82[EUR][1000 genomes]
rs545313	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs546967	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55971985	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56112646	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs566640	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61827540	0.87[EUR][1000 genomes]
rs7525075	0.83[EUR][1000 genomes]
rs947087	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][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	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
12	esv3419574	chr1:228397729-228402327	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
13	esv3397989	chr1:228398279-228402677	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
14	esv3361766	chr1:228399154-228401702	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
15	esv3358379	chr1:228399204-228403102	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2989563	OBSCN	cis	Esophagus Mucosa	GTEx
rs2989563	C1orf145	cis	Thyroid	GTEx
rs2989563	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228395800-228405200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr1:228398800-228402000	Active TSS	Psoas Muscle	Psoas
3	chr1:228400000-228401800	Active TSS	Thymus	Thymus
4	chr1:228400000-228402400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:228400000-228402600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:228400200-228401800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:228400200-228401800	Active TSS	Brain Angular Gyrus	brain
8	chr1:228400200-228402200	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:228400200-228402600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:228400400-228401800	Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr1:228400400-228401800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr1:228400400-228402000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr1:228400400-228402000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:228400400-228402000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:228400400-228402000	Active TSS	Fetal Kidney	kidney
16	chr1:228400400-228402000	Active TSS	NHEK	skin
17	chr1:228400400-228402200	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr1:228400400-228402400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:228400400-228403200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:228400600-228401800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:228400600-228401800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:228400600-228401800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:228400600-228401800	Active TSS	Fetal Intestine Small	intestine
24	chr1:228400600-228401800	Active TSS	Fetal Thymus	thymus
25	chr1:228400600-228401800	Active TSS	Gastric	stomach
26	chr1:228400600-228402000	Active TSS	H1 Cell Line	embryonic stem cell
27	chr1:228400600-228402000	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr1:228400600-228402000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:228400600-228402000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:228400600-228402000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:228400600-228402000	Active TSS	Brain Substantia Nigra	brain
32	chr1:228400600-228402000	Active TSS	Duodenum Mucosa	Duodenum
33	chr1:228400600-228402000	Active TSS	Fetal Lung	lung
34	chr1:228400600-228402200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:228400600-228402200	Active TSS	Fetal Intestine Large	intestine
36	chr1:228400600-228402200	Active TSS	Rectal Smooth Muscle	rectum
37	chr1:228400600-228402200	Active TSS	Hela-S3	cervix
38	chr1:228400600-228402400	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr1:228400600-228404200	Active TSS	Brain Anterior Caudate	brain
40	chr1:228400800-228401800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:228400800-228401800	Bivalent/Poised TSS	Fetal Stomach	stomach
42	chr1:228400800-228401800	Active TSS	Lung	lung
43	chr1:228400800-228401800	Flanking Active TSS	Right Ventricle	heart
44	chr1:228400800-228402000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:228400800-228402000	Active TSS	Fetal Brain Female	brain
46	chr1:228400800-228402000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:228400800-228402000	Active TSS	Placenta Amnion	Placenta Amnion
48	chr1:228400800-228402000	Active TSS	NH-A	brain
49	chr1:228400800-228402200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:228401000-228401800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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