Variant report

Variant	rs7549250
Chromosome Location	chr1:154404336-154404337
allele	C/T
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	TEAD4	chr1:154403950-154404714	K562	blood:	n/a	n/a
2	FOS	chr1:154403898-154404761	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:154403857-154404767	MCF10A-Er-Src	breast:	n/a	chr1:154404360-154404371
4	RCOR1	chr1:154404105-154404636	K562	blood:	n/a	n/a
5	CEBPB	chr1:154403903-154404613	IMR90	lung:	n/a	chr1:154404110-154404121
6	RUNX3	chr1:154404263-154404581	GM12878	blood:	n/a	n/a
7	JUN	chr1:154403983-154404491	Hela-S3	cervix:	n/a	n/a
8	RFX5	chr1:154404093-154404403	Hela-S3	cervix:	n/a	n/a
9	RUNX3	chr1:154403880-154404671	GM12878	blood:	n/a	n/a
10	TEAD4	chr1:154404039-154404515	ECC-1	luminal epithelium:	n/a	n/a
11	NR2F2	chr1:154404016-154404395	K562	blood:	n/a	n/a
12	MAFK	chr1:154404041-154404460	Hela-S3	cervix:	n/a	n/a
13	MYC	chr1:154403960-154404414	MCF10A-Er-Src	breast:	n/a	chr1:154404195-154404205
14	STAT3	chr1:154403894-154404751	MCF10A-Er-Src	breast:	n/a	chr1:154404360-154404371
15	MAX	chr1:154404018-154404482	Hela-S3	cervix:	n/a	chr1:154404195-154404205
16	MAZ	chr1:154404113-154404384	Hela-S3	cervix:	n/a	n/a
17	CHD2	chr1:154404073-154404427	Hela-S3	cervix:	n/a	n/a
18	STAT3	chr1:154404039-154404506	MCF10A-Er-Src	breast:	n/a	chr1:154404360-154404371
19	CEBPB	chr1:154403920-154404472	Hela-S3	cervix:	n/a	chr1:154404110-154404121
20	TEAD4	chr1:154404055-154404432	K562	blood:	n/a	n/a
21	CUX1	chr1:154404199-154404497	GM12878	blood:	n/a	n/a
22	RAD21	chr1:154403983-154404573	IMR90	lung:	n/a	n/a
23	FOS	chr1:154403898-154404697	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr1:154403894-154404760	MCF10A-Er-Src	breast:	n/a	chr1:154404360-154404371
25	EP300	chr1:154403889-154404666	ECC-1	luminal epithelium:	n/a	n/a
26	CREB1	chr1:154403979-154404376	GM12878	blood:	n/a	n/a
27	NR2F2	chr1:154403889-154404560	K562	blood:	n/a	n/a
28	TCF7L2	chr1:154404134-154404450	Hela-S3	cervix:	n/a	n/a
29	MYC	chr1:154404129-154404363	HUVEC	blood vessel:	n/a	chr1:154404195-154404205
30	RAD21	chr1:154404094-154404452	Hela-S3	cervix:	n/a	n/a
31	MAX	chr1:154403993-154404476	ECC-1	luminal epithelium:	n/a	chr1:154404195-154404205
32	FOS	chr1:154403901-154404739	MCF10A-Er-Src	breast:	n/a	n/a
33	MAX	chr1:154404062-154404351	K562	blood:	n/a	chr1:154404195-154404205
34	ATF1	chr1:154404090-154404446	K562	blood:	n/a	n/a
35	MXI1	chr1:154403529-154404726	IMR90	lung:	n/a	n/a
36	PBX3	chr1:154404023-154404475	SK-N-SH	brain:	n/a	n/a
37	EP300	chr1:154403946-154404437	Hela-S3	cervix:	n/a	n/a
38	TCF12	chr1:154404020-154404647	ECC-1	luminal epithelium:	n/a	n/a
39	EP300	chr1:154404098-154404468	K562	blood:	n/a	n/a
40	MYC	chr1:154403953-154404759	MCF10A-Er-Src	breast:	n/a	chr1:154404195-154404205
41	CBX3	chr1:154403988-154404410	K562	blood:	n/a	n/a
42	CREB1	chr1:154403966-154404443	K562	blood:	n/a	n/a
43	JUND	chr1:154403975-154404577	Hela-S3	cervix:	n/a	n/a
44	RCOR1	chr1:154404192-154404483	K562	blood:	n/a	n/a
45	MAFF	chr1:154404207-154404418	K562	blood:	n/a	n/a
46	BHLHE40	chr1:154404130-154404448	K562	blood:	n/a	n/a
47	MAX	chr1:154403987-154404528	ECC-1	luminal epithelium:	n/a	chr1:154404195-154404205
48	MAFK	chr1:154403935-154404487	IMR90	lung:	n/a	n/a
49	BRCA1	chr1:154404026-154404449	Hela-S3	cervix:	n/a	n/a
50	TEAD4	chr1:154403986-154404639	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154403886..154406138-chr1:154407625..154409567,2	K562	blood:
2	chr1:154390738..154393594-chr1:154404302..154405878,2	MCF-7	breast:
3	chr1:154383846..154386269-chr1:154404015..154406956,2	K562	blood:

Variant related genes	Relation type
IL6R	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10908837	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10908838	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265611	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11265612	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12117832	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12118721	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12118770	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12129500	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4553185	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4601580	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4845371	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845618	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845619	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845625	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59632925	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427658	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6667434	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6683206	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6686750	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6687726	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689306	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689393	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6694258	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6694817	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526131	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7536152	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7549338	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7549250	TMEM79	cis	parietal	SCAN
rs7549250	NPR1	cis	cerebellum	SCAN
rs7549250	SEMA6C	cis	parietal	SCAN
rs7549250	LINGO4	cis	parietal	SCAN
rs7549250	UBE2Q1	cis	cerebellum	SCAN
rs7549250	DENND4B	cis	cerebellum	SCAN
rs7549250	TDRD10	cis	lung	GTEx
rs7549250	PI4KB	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154393000-154405800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
2	chr1:154397000-154414200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:154399400-154405800	Enhancers	Right Atrium	heart
4	chr1:154399400-154407200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:154399600-154404400	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr1:154399600-154404800	Enhancers	Brain Germinal Matrix	brain
7	chr1:154399600-154406800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:154399600-154409200	Enhancers	Placenta	Placenta
9	chr1:154399800-154405600	Enhancers	Fetal Intestine Large	intestine
10	chr1:154399800-154405800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr1:154399800-154406200	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr1:154400600-154405200	Weak transcription	Fetal Thymus	thymus
13	chr1:154400800-154410600	Strong transcription	Primary T cells from cord blood	blood
14	chr1:154401000-154406000	Genic enhancers	Liver	Liver
15	chr1:154401200-154405000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:154401200-154406200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr1:154401200-154406600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
18	chr1:154401400-154404400	Weak transcription	Adipose Nuclei	Adipose
19	chr1:154401600-154405000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:154401600-154405600	Weak transcription	Fetal Lung	lung
21	chr1:154401800-154407000	Enhancers	NHEK	skin
22	chr1:154401800-154407200	Weak transcription	Pancreas	Pancrea
23	chr1:154402000-154405400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:154402000-154406600	Genic enhancers	Primary monocytes fromperipheralblood	blood
25	chr1:154402200-154404800	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr1:154402200-154405200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:154402200-154406200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:154402200-154406200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:154402200-154406800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:154402200-154407600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:154402400-154404400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:154402400-154404400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:154402400-154404600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr1:154402400-154405800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:154402400-154405800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:154402400-154406200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:154402400-154407200	Enhancers	HMEC	breast
38	chr1:154402400-154407800	Enhancers	Fetal Heart	heart
39	chr1:154402600-154404600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr1:154402600-154404600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:154402600-154404600	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:154402600-154405200	Weak transcription	Brain Anterior Caudate	brain
43	chr1:154402600-154405400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:154402600-154406200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr1:154402600-154407000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr1:154402600-154407400	Enhancers	NHDF-Ad	bronchial
47	chr1:154402800-154404400	Weak transcription	Brain Substantia Nigra	brain
48	chr1:154402800-154404800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr1:154402800-154405400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:154402800-154405400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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