Variant report

Variant	rs7553796
Chromosome Location	chr1:154404406-154404407
allele	A/C
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	RUNX3	chr1:154403880-154404671	GM12878	blood:	n/a	n/a
9	TEAD4	chr1:154404039-154404515	ECC-1	luminal epithelium:	n/a	n/a
10	MAFK	chr1:154404041-154404460	Hela-S3	cervix:	n/a	n/a
11	MYC	chr1:154403960-154404414	MCF10A-Er-Src	breast:	n/a	chr1:154404195-154404205
12	STAT3	chr1:154403894-154404751	MCF10A-Er-Src	breast:	n/a	chr1:154404360-154404371
13	MAX	chr1:154404018-154404482	Hela-S3	cervix:	n/a	chr1:154404195-154404205
14	CHD2	chr1:154404073-154404427	Hela-S3	cervix:	n/a	n/a
15	STAT3	chr1:154404039-154404506	MCF10A-Er-Src	breast:	n/a	chr1:154404360-154404371
16	CEBPB	chr1:154403920-154404472	Hela-S3	cervix:	n/a	chr1:154404110-154404121
17	TEAD4	chr1:154404055-154404432	K562	blood:	n/a	n/a
18	CUX1	chr1:154404199-154404497	GM12878	blood:	n/a	n/a
19	RAD21	chr1:154403983-154404573	IMR90	lung:	n/a	n/a
20	FOS	chr1:154403898-154404697	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr1:154403894-154404760	MCF10A-Er-Src	breast:	n/a	chr1:154404360-154404371
22	EP300	chr1:154403889-154404666	ECC-1	luminal epithelium:	n/a	n/a
23	NR2F2	chr1:154403889-154404560	K562	blood:	n/a	n/a
24	TCF7L2	chr1:154404134-154404450	Hela-S3	cervix:	n/a	n/a
25	RAD21	chr1:154404094-154404452	Hela-S3	cervix:	n/a	n/a
26	MAX	chr1:154403993-154404476	ECC-1	luminal epithelium:	n/a	chr1:154404195-154404205
27	FOS	chr1:154403901-154404739	MCF10A-Er-Src	breast:	n/a	n/a
28	ATF1	chr1:154404090-154404446	K562	blood:	n/a	n/a
29	MXI1	chr1:154403529-154404726	IMR90	lung:	n/a	n/a
30	PBX3	chr1:154404023-154404475	SK-N-SH	brain:	n/a	n/a
31	EP300	chr1:154403946-154404437	Hela-S3	cervix:	n/a	n/a
32	TCF12	chr1:154404020-154404647	ECC-1	luminal epithelium:	n/a	n/a
33	EP300	chr1:154404098-154404468	K562	blood:	n/a	n/a
34	MYC	chr1:154403953-154404759	MCF10A-Er-Src	breast:	n/a	chr1:154404195-154404205
35	CBX3	chr1:154403988-154404410	K562	blood:	n/a	n/a
36	CREB1	chr1:154403966-154404443	K562	blood:	n/a	n/a
37	JUND	chr1:154403975-154404577	Hela-S3	cervix:	n/a	n/a
38	RCOR1	chr1:154404192-154404483	K562	blood:	n/a	n/a
39	MAFF	chr1:154404207-154404418	K562	blood:	n/a	n/a
40	BHLHE40	chr1:154404130-154404448	K562	blood:	n/a	n/a
41	MAX	chr1:154403987-154404528	ECC-1	luminal epithelium:	n/a	chr1:154404195-154404205
42	MAFK	chr1:154403935-154404487	IMR90	lung:	n/a	n/a
43	BRCA1	chr1:154404026-154404449	Hela-S3	cervix:	n/a	n/a
44	TEAD4	chr1:154403986-154404639	ECC-1	luminal epithelium:	n/a	n/a
45	MAX	chr1:154404049-154404414	K562	blood:	n/a	chr1:154404195-154404205
46	STAT3	chr1:154404004-154404469	Hela-S3	cervix:	n/a	chr1:154404360-154404371
47	JUN	chr1:154403977-154404831	K562	blood:	n/a	n/a
48	RCOR1	chr1:154402901-154404914	IMR90	lung:	n/a	n/a
49	SMC3	chr1:154403764-154404536	Hela-S3	cervix:	n/a	n/a
50	GTF2F1	chr1:154404030-154404461	Hela-S3	cervix:	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: 1 )

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

rs_ID	r²[population]
rs10908837	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10908838	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265611	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11265612	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12117832	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12118721	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12118770	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12129500	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4553185	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4601580	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4845371	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845618	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845619	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845625	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59632925	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427658	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6667434	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6683206	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6686750	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6687726	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689306	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689393	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6694258	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6694817	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526131	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7536152	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7549250	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]
rs7549338	0.91[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]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7553796	TDRD10	cis	lung	GTEx

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	chr1:154399600-154404800	Enhancers	Brain Germinal Matrix	brain
6	chr1:154399600-154406800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:154399600-154409200	Enhancers	Placenta	Placenta
8	chr1:154399800-154405600	Enhancers	Fetal Intestine Large	intestine
9	chr1:154399800-154405800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr1:154399800-154406200	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr1:154400600-154405200	Weak transcription	Fetal Thymus	thymus
12	chr1:154400800-154410600	Strong transcription	Primary T cells from cord blood	blood
13	chr1:154401000-154406000	Genic enhancers	Liver	Liver
14	chr1:154401200-154405000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:154401200-154406200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:154401200-154406600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
17	chr1:154401600-154405000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:154401600-154405600	Weak transcription	Fetal Lung	lung
19	chr1:154401800-154407000	Enhancers	NHEK	skin
20	chr1:154401800-154407200	Weak transcription	Pancreas	Pancrea
21	chr1:154402000-154405400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:154402000-154406600	Genic enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:154402200-154404800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:154402200-154405200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:154402200-154406200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:154402200-154406200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:154402200-154406800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:154402200-154407600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr1:154402400-154404600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr1:154402400-154405800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:154402400-154405800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr1:154402400-154406200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:154402400-154407200	Enhancers	HMEC	breast
34	chr1:154402400-154407800	Enhancers	Fetal Heart	heart
35	chr1:154402600-154404600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:154402600-154404600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:154402600-154404600	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:154402600-154405200	Weak transcription	Brain Anterior Caudate	brain
39	chr1:154402600-154405400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:154402600-154406200	Enhancers	H1 Cell Line	embryonic stem cell
41	chr1:154402600-154407000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:154402600-154407400	Enhancers	NHDF-Ad	bronchial
43	chr1:154402800-154404800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr1:154402800-154405400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:154402800-154405400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:154402800-154405600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:154402800-154405800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:154402800-154406200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:154402800-154407200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:154403000-154404800	Enhancers	K562	blood

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