Variant report

Variant	rs7183977
Chromosome Location	chr15:40377092-40377093
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	FOS	chr15:40376876-40377271	Hela-S3	cervix:	n/a	chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377092 chr15:40377083-40377093
2	CEBPB	chr15:40376822-40377153	Hela-S3	cervix:	n/a	n/a
3	RCOR1	chr15:40376828-40377186	Hela-S3	cervix:	n/a	n/a
4	MAX	chr15:40376822-40377819	Hela-S3	cervix:	n/a	chr15:40377084-40377093
5	MAX	chr15:40376835-40377201	Hela-S3	cervix:	n/a	chr15:40377084-40377093
6	FOS	chr15:40376800-40377232	MCF10A-Er-Src	breast:	n/a	chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377092 chr15:40377083-40377093
7	POLR2A	chr15:40376812-40377251	Hela-S3	cervix:	n/a	n/a
8	FOS	chr15:40376788-40377222	MCF10A-Er-Src	breast:	n/a	chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377092 chr15:40377083-40377093
9	SMC3	chr15:40376804-40377273	Hela-S3	cervix:	n/a	n/a
10	FOS	chr15:40376815-40377168	MCF10A-Er-Src	breast:	n/a	chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377092 chr15:40377083-40377093
11	RAD21	chr15:40376808-40377249	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr15:40376980-40377159	Hela-S3	cervix:	n/a	n/a
13	MAZ	chr15:40376914-40377195	Hela-S3	cervix:	n/a	chr15:40377084-40377093
14	USF2	chr15:40376976-40377240	Hela-S3	cervix:	n/a	n/a
15	MYC	chr15:40376948-40377111	Hela-S3	cervix:	n/a	chr15:40377084-40377093
16	FOS	chr15:40376795-40377206	MCF10A-Er-Src	breast:	n/a	chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377092 chr15:40377083-40377093
17	JUND	chr15:40376786-40377669	Hela-S3	cervix:	n/a	chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377092 chr15:40377083-40377093
18	TCF12	chr15:40376685-40377292	ECC-1	luminal epithelium:	n/a	n/a
19	JUN	chr15:40376797-40377214	Hela-S3	cervix:	n/a	chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377092 chr15:40377083-40377093
20	EP300	chr15:40376680-40377444	ECC-1	luminal epithelium:	n/a	chr15:40377084-40377093
21	CTCF	chr15:40376994-40377160	NHEK	skin:	n/a	n/a
22	EP300	chr15:40376774-40377185	Hela-S3	cervix:	n/a	chr15:40377084-40377093
23	GTF2F1	chr15:40376875-40377347	Hela-S3	cervix:	n/a	n/a
24	FOSL1	chr15:40376774-40377375	HCT-116	colon:	n/a	chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377092 chr15:40377083-40377093
25	E2F4	chr15:40377007-40377134	MCF10A-Er-Src	breast:	n/a	n/a
26	MYC	chr15:40376891-40377144	MCF10A-Er-Src	breast:	n/a	chr15:40377084-40377093
27	JUND	chr15:40376762-40377306	HCT-116	colon:	n/a	chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377093 chr15:40377083-40377092 chr15:40377083-40377093
28	RFX5	chr15:40376839-40377237	Hela-S3	cervix:	n/a	n/a
29	CHD2	chr15:40376838-40377196	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40376791..40380091-chr15:40393802..40397569,3	MCF-7	breast:
2	chr15:40371046..40373186-chr15:40375916..40377601,2	MCF-7	breast:
3	chr15:40373200..40375789-chr15:40377087..40378964,2	MCF-7	breast:
4	chr15:40375380..40377827-chr15:40379626..40381482,2	K562	blood:

Variant related genes	Relation type
ENSG00000259409	TF binding region
ENSG00000259409	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1010879	1.00[ASN][1000 genomes]
rs11631442	1.00[ASN][1000 genomes]
rs11638521	0.88[EUR][1000 genomes]
rs12899649	1.00[CHB][hapmap]
rs12912442	1.00[CHB][hapmap]
rs16924528	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17722502	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17722526	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17723133	0.82[CEU][hapmap]
rs2412456	1.00[ASW][hapmap];1.00[CHB][hapmap]
rs2412478	1.00[ASN][1000 genomes]
rs28444847	1.00[ASN][1000 genomes]
rs28479712	0.90[EUR][1000 genomes]
rs28515996	1.00[ASN][1000 genomes]
rs28534747	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28587891	0.90[EUR][1000 genomes]
rs28620926	0.89[EUR][1000 genomes]
rs28736699	1.00[ASN][1000 genomes]
rs28826672	1.00[ASN][1000 genomes]
rs35781999	1.00[ASN][1000 genomes]
rs3923235	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4497657	1.00[ASN][1000 genomes]
rs4923852	1.00[ASW][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924410	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4924413	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4924415	0.88[EUR][1000 genomes]
rs4924416	0.89[EUR][1000 genomes]
rs4924417	1.00[ASN][1000 genomes]
rs62004158	1.00[ASN][1000 genomes]
rs71132133	1.00[ASN][1000 genomes]
rs7181230	0.95[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs72731415	1.00[ASN][1000 genomes]
rs7497289	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs749748	1.00[ASN][1000 genomes]
rs8026641	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs937213	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9919974	1.00[ASN][1000 genomes]
rs9972424	0.95[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs9972442	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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 target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7183977	C15orf41	cis	parietal	SCAN
rs7183977	FSIP1	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40373800-40378800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:40374200-40381400	Enhancers	Fetal Thymus	thymus
3	chr15:40374200-40388200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:40374400-40377800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:40374400-40379000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:40374600-40377800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:40374600-40377800	Enhancers	Primary T cells from cord blood	blood
8	chr15:40374600-40379200	Weak transcription	Aorta	Aorta
9	chr15:40374800-40377600	Enhancers	Primary B cells from peripheral blood	blood
10	chr15:40374800-40377600	Enhancers	Thymus	Thymus
11	chr15:40374800-40377600	Weak transcription	HMEC	breast
12	chr15:40374800-40379400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:40374800-40380400	Weak transcription	Ovary	ovary
14	chr15:40374800-40380600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:40374800-40382000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:40374800-40383800	Weak transcription	Brain Substantia Nigra	brain
17	chr15:40375000-40377400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:40375000-40377400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:40375000-40378600	Weak transcription	Psoas Muscle	Psoas
20	chr15:40375000-40378800	Weak transcription	Right Atrium	heart
21	chr15:40375000-40378800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:40375000-40379200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:40375000-40380800	Weak transcription	NHLF	lung
24	chr15:40375000-40382200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:40375000-40383600	Weak transcription	Brain Anterior Caudate	brain
26	chr15:40375000-40383800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr15:40375000-40384200	Weak transcription	Brain Angular Gyrus	brain
28	chr15:40375200-40377400	Weak transcription	Right Ventricle	heart
29	chr15:40375200-40378400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:40375200-40378800	Weak transcription	Colon Smooth Muscle	Colon
31	chr15:40375200-40378800	Weak transcription	Pancreas	Pancrea
32	chr15:40375200-40378800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:40375200-40378800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:40375200-40379000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr15:40375200-40380800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr15:40375200-40381800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:40375400-40377800	Enhancers	HepG2	liver
38	chr15:40375400-40380600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:40375800-40377200	Weak transcription	Esophagus	oesophagus
40	chr15:40375800-40380200	Weak transcription	Spleen	Spleen
41	chr15:40375800-40380400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:40376000-40377400	Weak transcription	Colonic Mucosa	Colon
43	chr15:40376000-40377400	Weak transcription	Fetal Stomach	stomach
44	chr15:40376000-40379200	Weak transcription	Fetal Intestine Small	intestine
45	chr15:40376000-40379600	Weak transcription	Fetal Intestine Large	intestine
46	chr15:40376000-40380400	Weak transcription	Lung	lung
47	chr15:40376000-40383600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr15:40376200-40377200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:40376200-40377200	Weak transcription	Fetal Kidney	kidney
50	chr15:40376200-40377400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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