Variant report

Variant	rs7167854
Chromosome Location	chr15:41038214-41038215
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	POLR2A	chr15:41037757-41038470	HL-60	blood:	n/a	n/a
2	MAFK	chr15:41037952-41038361	K562	blood:	n/a	n/a
3	NR2F2	chr15:41037761-41038415	K562	blood:	n/a	n/a
4	POLR2A	chr15:41037814-41038463	HL-60	blood:	n/a	n/a
5	EP300	chr15:41037884-41038405	K562	blood:	n/a	n/a
6	MAX	chr15:41037846-41038255	K562	blood:	n/a	n/a
7	CEBPD	chr15:41037860-41038404	K562	blood:	n/a	n/a
8	POLR2A	chr15:41037899-41038353	K562	blood:	n/a	n/a
9	NR2F2	chr15:41037822-41038319	K562	blood:	n/a	n/a
10	TEAD4	chr15:41037862-41038439	K562	blood:	n/a	n/a
11	POLR2A	chr15:41037965-41038322	Hela-S3	cervix:	n/a	n/a
12	SPI1	chr15:41037931-41038447	HL-60	blood:	n/a	chr15:41038301-41038310 chr15:41038302-41038309
13	TAL1	chr15:41037825-41038471	K562	blood:	n/a	chr15:41037997-41038015
14	MAZ	chr15:41037942-41038274	K562	blood:	n/a	n/a
15	MAX	chr15:41037935-41038320	K562	blood:	n/a	n/a
16	ATF1	chr15:41037889-41038285	K562	blood:	n/a	n/a
17	MEF2A	chr15:41038183-41038457	GM12878	blood:	n/a	chr15:41038365-41038379 chr15:41038360-41038381 chr15:41038360-41038381
18	RCOR1	chr15:41037910-41038394	K562	blood:	n/a	n/a
19	POLR2A	chr15:41037842-41038363	K562	blood:	n/a	n/a
20	GATA1	chr15:41037682-41039421	PBDE	blood:	n/a	chr15:41037997-41038006 chr15:41037993-41038009 chr15:41038373-41038382 chr15:41037998-41038015 chr15:41038370-41038386 chr15:41038375-41038382 chr15:41038368-41038389 chr15:41038370-41038386 chr15:41038375-41038385
21	POLR2A	chr15:41037903-41038959	PBDE	blood:	n/a	n/a
22	POLR2A	chr15:41037819-41038353	K562	blood:	n/a	n/a
23	TEAD4	chr15:41037827-41038496	K562	blood:	n/a	n/a
24	POLR2A	chr15:41037908-41038335	K562	blood:	n/a	n/a
25	POLR2A	chr15:41037857-41038237	K562	blood:	n/a	n/a
26	MYC	chr15:41037885-41038387	K562	blood:	n/a	n/a
27	JUND	chr15:41037987-41038349	K562	blood:	n/a	n/a
28	PML	chr15:41037761-41038377	K562	blood:	n/a	n/a
29	PML	chr15:41037873-41038254	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41031017..41033907-chr15:41037060..41039542,3	MCF-7	breast:
2	chr15:41037003..41039062-chr15:41068615..41070670,2	MCF-7	breast:
3	chr15:40986478..40988882-chr15:41036813..41039846,3	K562	blood:
4	chr15:41036885..41040237-chr15:41045392..41049336,5	MCF-7	breast:
5	chr15:41037589..41040458-chr15:41068418..41070751,2	K562	blood:
6	chr15:41035271..41040468-chr15:41046040..41049485,6	MCF-7	breast:
7	chr15:41036948..41038953-chr15:41054723..41057087,2	K562	blood:
8	chr15:41036541..41039505-chr15:41136514..41138272,3	MCF-7	breast:

Variant related genes	Relation type
RMDN3	TF binding region
ENSG00000166145	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000245849	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000051180	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10775121	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631563	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11855560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858337	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11858338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12372947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439683	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441514	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12442845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12593359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12908284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12912742	0.89[ASN][1000 genomes]
rs2263551	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412548	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412549	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2577564	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2619679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619680	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2917955	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2928140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3092982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3092983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3101861	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34400306	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36106105	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs45495293	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4923884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924493	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924495	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56042757	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492961	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7164339	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7169010	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173646	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174551	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7175401	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs752012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025883	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033829	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8036817	0.93[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	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7167854	C15orf57	cis	Nerve Tibial	GTEx
rs7167854	C15orf57	cis	Adipose Subcutaneous	GTEx
rs7167854	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs7167854	C15orf57	cis	Artery Aorta	GTEx
rs7167854	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs7167854	C15orf57	cis	Artery Tibial	GTEx
rs7167854	RAD51	cis	multi-tissue	Pritchard
rs7167854	RP11-111A22.1	cis	Artery Tibial	GTEx
rs7167854	C15orf57	cis	Esophagus Muscularis	GTEx
rs7167854	C15orf57	cis	lung	GTEx
rs7167854	CCDC32	cis	multi-tissue	Pritchard
rs7167854	RP11-111A22.1	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41008200-41046600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:41019400-41046200	Strong transcription	Fetal Stomach	stomach
3	chr15:41020000-41043600	Strong transcription	Dnd41	blood
4	chr15:41020800-41045400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr15:41021800-41044600	Strong transcription	Brain Germinal Matrix	brain
6	chr15:41023200-41045200	Strong transcription	Thymus	Thymus
7	chr15:41023800-41038400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:41023800-41045200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:41025600-41045000	Strong transcription	Primary T cells from cord blood	blood
10	chr15:41025600-41045400	Strong transcription	Stomach Smooth Muscle	stomach
11	chr15:41026000-41044600	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:41026200-41044600	Strong transcription	Lung	lung
13	chr15:41026800-41045200	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr15:41027200-41038400	Strong transcription	Brain Hippocampus Middle	brain
15	chr15:41029000-41041800	Weak transcription	Fetal Kidney	kidney
16	chr15:41030800-41044000	Weak transcription	Psoas Muscle	Psoas
17	chr15:41031000-41046600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:41032000-41043000	Weak transcription	Fetal Brain Male	brain
19	chr15:41032600-41046200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:41032600-41046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:41032600-41046600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:41033200-41039200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:41033200-41042000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr15:41034000-41038400	Strong transcription	Aorta	Aorta
25	chr15:41034200-41038400	Strong transcription	Brain Angular Gyrus	brain
26	chr15:41034200-41045800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr15:41034400-41044400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:41034400-41044600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:41034400-41045200	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:41034600-41044800	Strong transcription	Brain Substantia Nigra	brain
31	chr15:41034600-41045800	Genic enhancers	Fetal Intestine Small	intestine
32	chr15:41034800-41038400	Strong transcription	HepG2	liver
33	chr15:41034800-41038600	Strong transcription	Esophagus	oesophagus
34	chr15:41034800-41044400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr15:41034800-41044600	Strong transcription	Fetal Brain Female	brain
36	chr15:41034800-41046200	Genic enhancers	Fetal Intestine Large	intestine
37	chr15:41035600-41039800	Strong transcription	Ovary	ovary
38	chr15:41035600-41040600	Genic enhancers	K562	blood
39	chr15:41035800-41038400	Strong transcription	Colon Smooth Muscle	Colon
40	chr15:41035800-41039800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:41035800-41046600	Weak transcription	Right Atrium	heart
42	chr15:41036000-41038400	Strong transcription	Rectal Smooth Muscle	rectum
43	chr15:41036000-41040400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr15:41036200-41041000	Strong transcription	Gastric	stomach
45	chr15:41036600-41040400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:41036600-41041600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:41036600-41042800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:41036600-41042800	Weak transcription	HSMMtube	muscle
49	chr15:41036600-41043000	Weak transcription	HMEC	breast
50	chr15:41036600-41044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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