Variant report

Variant	rs61828088
Chromosome Location	chr1:174768522-174768523
allele	A/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	KAP1	chr1:174768365-174770087	HEK293	kidney:	n/a	n/a
2	STAT3	chr1:174768193-174768629	MCF10A-Er-Src	breast:	n/a	chr1:174768362-174768373 chr1:174768364-174768372
3	BCLAF1	chr1:174768356-174769647	GM12878	blood:	n/a	chr1:174769257-174769266 chr1:174769263-174769272
4	TAF1	chr1:174768362-174770036	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr1:174768265-174769500	PFSK-1	brain:	n/a	n/a
6	MAX	chr1:174768521-174769193	SK-N-SH	brain:	n/a	n/a
7	KAP1	chr1:174768412-174769308	U2OS	brain:	n/a	n/a
8	TAF1	chr1:174768511-174769344	PFSK-1	brain:	n/a	n/a
9	REST	chr1:174768351-174769631	H1-neurons	neurons:	n/a	n/a
10	STAT3	chr1:174768204-174768866	MCF10A-Er-Src	breast:	n/a	chr1:174768362-174768373 chr1:174768364-174768372
11	SIN3AK20	chr1:174768510-174769216	PFSK-1	brain:	n/a	n/a
12	REST	chr1:174768060-174770788	H1-neurons	neurons:	n/a	n/a
13	MTA3	chr1:174768312-174769621	GM12878	blood:	n/a	n/a
14	FOS	chr1:174768262-174768992	MCF10A-Er-Src	breast:	n/a	n/a
15	MTA3	chr1:174768451-174769365	GM12878	blood:	n/a	n/a
16	USF1	chr1:174768521-174768787	SK-N-SH_RA	brain:	n/a	n/a
17	CEBPB	chr1:174768512-174769088	H1-hESC	embryonic stem cell:	n/a	n/a
18	CEBPB	chr1:174768356-174769457	GM12878	blood:	n/a	chr1:174768414-174768427
19	BCLAF1	chr1:174768460-174769315	GM12878	blood:	n/a	chr1:174769257-174769266 chr1:174769263-174769272
20	USF1	chr1:174768484-174768851	SK-N-SH_RA	brain:	n/a	n/a
21	CEBPB	chr1:174768253-174769171	IMR90	lung:	n/a	chr1:174768414-174768427
22	STAT3	chr1:174768281-174768817	MCF10A-Er-Src	breast:	n/a	chr1:174768362-174768373 chr1:174768364-174768372
23	FOS	chr1:174768275-174769053	MCF10A-Er-Src	breast:	n/a	n/a
24	USF2	chr1:174768497-174769052	GM12878	blood:	n/a	n/a
25	USF1	chr1:174768483-174769074	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:174768466-174769302	PFSK-1	brain:	n/a	n/a
27	NFATC1	chr1:174768499-174769394	GM12878	blood:	n/a	n/a
28	FOXM1	chr1:174768409-174769678	GM12878	blood:	n/a	n/a
29	ATF2	chr1:174768311-174769484	GM12878	blood:	n/a	n/a
30	MYC	chr1:174768350-174768992	MCF10A-Er-Src	breast:	n/a	n/a
31	SETDB1	chr1:174768401-174768995	U2OS	brain:	n/a	n/a
32	PML	chr1:174768431-174769421	GM12878	blood:	n/a	n/a
33	NFIC	chr1:174768451-174769454	GM12878	blood:	n/a	n/a
34	MXI1	chr1:174768186-174770204	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr1:174768353-174770468	H1-neurons	neurons:	n/a	n/a
36	NFATC1	chr1:174768427-174769442	GM12878	blood:	n/a	n/a
37	STAT3	chr1:174768037-174768843	MCF10A-Er-Src	breast:	n/a	chr1:174768362-174768373 chr1:174768364-174768372
38	STAT3	chr1:174768513-174769401	GM12878	blood:	n/a	chr1:174769009-174769017
39	MAZ	chr1:174768350-174769792	IMR90	lung:	n/a	n/a
40	RUNX3	chr1:174768368-174769375	GM12878	blood:	n/a	n/a
41	STAT5A	chr1:174768486-174769644	GM12878	blood:	n/a	chr1:174769009-174769017
42	MYC	chr1:174768511-174769083	MCF10A-Er-Src	breast:	n/a	n/a
43	CEBPB	chr1:174768245-174768597	A549	lung:	n/a	chr1:174768414-174768427
44	IKZF1	chr1:174768447-174769167	GM12878	blood:	n/a	n/a
45	FOS	chr1:174768280-174769016	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr1:174768248-174768993	MCF10A-Er-Src	breast:	n/a	n/a
47	ATF2	chr1:174768485-174769398	GM12878	blood:	n/a	n/a
48	EBF1	chr1:174768460-174769273	GM12878	blood:	n/a	chr1:174768801-174768812 chr1:174768802-174768812
49	MAFK	chr1:174768295-174769141	IMR90	lung:	n/a	n/a
50	POLR2A	chr1:174768263-174770522	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174768282..174770482-chr1:174964486..174966155,2	MCF-7	breast:
2	chr1:174766907..174768674-chr1:174967181..174969614,2	K562	blood:

Variant related genes	Relation type
RABGAP1L	TF binding region
ENSG00000252552	Chromatin interaction
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1002125	0.81[AMR][1000 genomes]
rs10158096	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10489333	0.81[AMR][1000 genomes]
rs10494493	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912849	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10912850	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12063802	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12065854	0.85[EUR][1000 genomes]
rs12066247	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12068637	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12087589	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12563930	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12565810	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12566477	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12568182	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs16847257	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs16847271	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs16847402	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16847450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16847563	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16847633	0.81[AMR][1000 genomes]
rs28660133	0.81[AMR][1000 genomes]
rs34952844	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35216639	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs41524947	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57353443	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57366106	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61826902	1.00[AFR][1000 genomes]
rs61826904	1.00[AFR][1000 genomes]
rs61826909	0.81[EUR][1000 genomes]
rs61826913	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs61826917	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61826918	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs61826923	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs61826924	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61826925	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61826941	0.84[EUR][1000 genomes]
rs61826942	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61826949	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61826950	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61826951	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61826952	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61826953	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61826956	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61826957	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61826959	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828062	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828064	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61828065	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61828068	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828081	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61828117	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61828121	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828143	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828144	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61828148	0.81[AMR][1000 genomes]
rs61828149	0.87[AFR][1000 genomes]
rs61828151	0.81[AMR][1000 genomes]
rs61828156	1.00[AFR][1000 genomes]
rs7523516	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv548198	chr1:174731596-174800872	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv1824383	chr1:174764839-174801748	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1844306	chr1:174764839-174801748	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv1819206	chr1:174764839-174802731	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv1844208	chr1:174764839-174818547	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv1847553	chr1:174764839-174818547	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61828088	SERPINC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174765000-174768800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:174766800-174768600	Weak transcription	K562	blood
3	chr1:174767000-174768600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:174767000-174768600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:174767000-174768800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:174767200-174768600	Weak transcription	Spleen	Spleen
7	chr1:174768000-174768600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:174768000-174768600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:174768000-174768600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:174768000-174768600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:174768200-174768600	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:174768200-174768600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:174768200-174768600	Flanking Active TSS	Brain Germinal Matrix	brain
14	chr1:174768200-174768600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:174768200-174768600	Enhancers	Rectal Smooth Muscle	rectum
16	chr1:174768200-174768600	Enhancers	HSMM	muscle
17	chr1:174768200-174768800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr1:174768200-174768800	Flanking Active TSS	GM12878-XiMat	blood
19	chr1:174768200-174769000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:174768200-174769000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:174768200-174769600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:174768200-174770000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr1:174768200-174770400	Active TSS	Stomach Smooth Muscle	stomach
24	chr1:174768400-174768600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr1:174768400-174768600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:174768400-174768600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:174768400-174768600	Enhancers	Primary B cells from cord blood	blood
28	chr1:174768400-174768600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:174768400-174768600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr1:174768400-174768600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr1:174768400-174768600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:174768400-174768600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr1:174768400-174768600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:174768400-174768600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr1:174768400-174768600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:174768400-174768600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:174768400-174768600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:174768400-174768600	Enhancers	Liver	Liver
39	chr1:174768400-174768600	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr1:174768400-174768600	Active TSS	Fetal Brain Male	brain
41	chr1:174768400-174768600	Flanking Active TSS	Fetal Intestine Large	intestine
42	chr1:174768400-174768600	Enhancers	Left Ventricle	heart
43	chr1:174768400-174768600	Enhancers	Pancreas	Pancrea
44	chr1:174768400-174768600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr1:174768400-174768600	Flanking Active TSS	HSMMtube	muscle
46	chr1:174768400-174768800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:174768400-174768800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:174768400-174768800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr1:174768400-174768800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:174768400-174768800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell

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