Variant report

Variant	rs11631813
Chromosome Location	chr15:82555242-82555243
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	chr15:82554018-82555291	U87	brain:	n/a	n/a
2	SRF	chr15:82554718-82555450	MCF-7	breast:	n/a	n/a
3	ELK4	chr15:82554215-82555334	Hela-S3	cervix:	n/a	chr15:82555110-82555121
4	ZNF143	chr15:82554803-82555245	GM12878	blood:	n/a	n/a
5	EBF1	chr15:82555027-82555265	GM12878	blood:	n/a	n/a
6	SMARCC1	chr15:82554343-82555431	Hela-S3	cervix:	n/a	n/a
7	HEY1	chr15:82554732-82555254	HepG2	liver:	n/a	chr15:82554844-82554859
8	POLR2A	chr15:82554662-82555249	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:82554686-82555363	A549	lung:	n/a	n/a
10	ELF1	chr15:82554539-82555429	GM12878	blood:	n/a	n/a
11	ELF1	chr15:82554707-82555317	MCF-7	breast:	n/a	n/a
12	BRCA1	chr15:82554360-82555242	Hela-S3	cervix:	n/a	n/a
13	TAF1	chr15:82554359-82555295	A549	lung:	n/a	n/a
14	RFX5	chr15:82554804-82555317	Hela-S3	cervix:	n/a	chr15:82555150-82555165 chr15:82555149-82555166 chr15:82555150-82555165 chr15:82555150-82555165
15	MXI1	chr15:82553678-82556137	SK-N-SH	brain:	n/a	chr15:82555149-82555164 chr15:82555151-82555166
16	TCF3	chr15:82554681-82555254	GM12878	blood:	n/a	n/a
17	NR2C2	chr15:82554803-82555375	GM12878	blood:	n/a	chr15:82555084-82555093 chr15:82555081-82555096 chr15:82555082-82555095
18	SIN3AK20	chr15:82554230-82555462	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr15:82554593-82555383	SK-N-MC	brain:	n/a	n/a
20	CREB1	chr15:82554741-82555422	HepG2	liver:	n/a	n/a
21	YY1	chr15:82554768-82555412	GM12892	blood:	n/a	chr15:82554790-82554801 chr15:82555293-82555307
22	POLR2A	chr15:82554644-82555286	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr15:82554724-82555371	K562	blood:	n/a	n/a
24	PBX3	chr15:82554826-82555357	SK-N-SH	brain:	n/a	n/a
25	MXI1	chr15:82554368-82555388	HepG2	liver:	n/a	chr15:82555149-82555164 chr15:82555151-82555166
26	YY1	chr15:82554607-82555332	H1-hESC	embryonic stem cell:	n/a	chr15:82554790-82554801 chr15:82555293-82555307
27	JUND	chr15:82554783-82555292	K562	blood:	n/a	n/a
28	MYC	chr15:82554911-82555254	MCF-7	breast:	n/a	n/a
29	GTF2F1	chr15:82554911-82555279	Hela-S3	cervix:	n/a	n/a
30	YY1	chr15:82554795-82555332	GM12878	blood:	n/a	chr15:82555293-82555307
31	RCOR1	chr15:82554185-82555306	K562	blood:	n/a	n/a
32	POLR2A	chr15:82554339-82555329	NB4	blood:	n/a	n/a
33	HA-E2F1	chr15:82554361-82555384	MCF-7	breast:	n/a	n/a
34	REST	chr15:82554607-82555488	H1-neurons	neurons:	n/a	chr15:82554610-82554623
35	POLR2A	chr15:82554684-82555286	GM10847	blood:	n/a	n/a
36	TBL1XR1	chr15:82554832-82555287	GM12878	blood:	n/a	n/a
37	EP300	chr15:82554931-82555247	GM12878	blood:	n/a	chr15:82555118-82555127
38	HEY1	chr15:82554727-82555286	K562	blood:	n/a	chr15:82554844-82554859
39	ATF1	chr15:82554940-82555263	K562	blood:	n/a	n/a
40	POLR2A	chr15:82554153-82555334	Hela-S3	cervix:	n/a	n/a
41	WRNIP1	chr15:82555010-82555292	GM12878	blood:	n/a	n/a
42	EGR1	chr15:82554663-82555335	HCT-116	colon:	n/a	chr15:82554900-82554907
43	POLR2A	chr15:82554720-82555311	HCT-116	colon:	n/a	n/a
44	MXI1	chr15:82554640-82555425	GM12878	blood:	n/a	chr15:82555149-82555164 chr15:82555151-82555166
45	POLR2A	chr15:82554334-82555393	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr15:82554547-82555528	PFSK-1	brain:	n/a	n/a
47	ETS1	chr15:82554800-82555304	K562	blood:	n/a	n/a
48	MAZ	chr15:82554322-82555352	Hela-S3	cervix:	n/a	chr15:82554639-82554650 chr15:82554640-82554649
49	TAF1	chr15:82554725-82555248	K562	blood:	n/a	n/a
50	GABPA	chr15:82554649-82555413	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:82554707..82555430-chr17:57915266..57915873,2	MCF-7	breast:

Variant related genes	Relation type
FAM154B	TF binding region
EFTUD1	TF binding region
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11073036	0.92[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11630197	0.91[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11633000	0.85[ASN][1000 genomes]
rs11639440	0.94[JPT][hapmap]
rs11854289	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11854483	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12324875	0.90[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs1501367	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1566559	0.81[ASN][1000 genomes]
rs1566560	0.81[ASN][1000 genomes]
rs1566561	0.95[ASN][1000 genomes]
rs16973457	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1846908	0.81[ASN][1000 genomes]
rs1948741	0.92[ASN][1000 genomes]
rs1948742	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs1972460	0.92[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2016372	0.96[ASN][1000 genomes]
rs2047679	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2134046	0.90[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2457497	0.81[ASW][hapmap];0.85[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2665103	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs28454949	0.86[ASN][1000 genomes]
rs28522807	0.89[ASN][1000 genomes]
rs3759800	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs3858953	0.87[ASN][1000 genomes]
rs3902959	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4238534	0.91[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4267268	0.94[ASN][1000 genomes]
rs4296215	0.83[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778674	0.87[ASN][1000 genomes]
rs4778986	0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs4778987	0.90[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs4778990	0.87[ASN][1000 genomes]
rs56398167	0.92[ASN][1000 genomes]
rs61554133	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7167504	0.93[ASN][1000 genomes]
rs7176926	0.83[ASN][1000 genomes]
rs72749540	0.92[ASN][1000 genomes]
rs72749557	0.93[ASN][1000 genomes]
rs72749560	0.93[ASN][1000 genomes]
rs72749561	0.93[ASN][1000 genomes]
rs72749564	0.94[ASN][1000 genomes]
rs72749575	0.90[ASN][1000 genomes]
rs72749586	0.96[ASN][1000 genomes]
rs7403041	0.87[ASN][1000 genomes]
rs7403244	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8025964	0.90[ASN][1000 genomes]
rs8027301	0.81[ASW][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs8027661	0.81[ASW][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs8030210	0.92[ASN][1000 genomes]
rs8030250	0.92[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs8032633	0.92[ASN][1000 genomes]
rs8033313	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs905450	0.81[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs9972440	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457212	chr15:82454283-82573255	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv570243	chr15:82454283-82573255	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv457213	chr15:82456227-82573255	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv570244	chr15:82456227-82573255	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv570245	chr15:82456227-82591082	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1041040	chr15:82465124-82606410	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1801737	chr15:82468455-82589044	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv570246	chr15:82485707-82581264	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1041506	chr15:82496164-82581427	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv1798145	chr15:82506790-82581264	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv904440	chr15:82524544-82591082	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv904441	chr15:82532963-82580736	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv904442	chr15:82540174-82571046	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv1054025	chr15:82540486-83058214	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	nsv904443	chr15:82553472-82571780	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11631813	FAM154B	cis	parietal	SCAN
rs11631813	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL
rs11631813	EPS8	trans	parietal	SCAN
rs11631813	ADAMTS7	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82552400-82556800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:82553400-82555400	Active TSS	Right Ventricle	heart
3	chr15:82553400-82555800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:82553400-82555800	Active TSS	Psoas Muscle	Psoas
5	chr15:82553400-82555800	Active TSS	HSMMtube	muscle
6	chr15:82553600-82555600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr15:82553600-82555600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:82553600-82555800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:82553600-82556000	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr15:82553800-82555800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr15:82553800-82556200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr15:82554000-82555600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:82554000-82555600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:82554000-82555600	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr15:82554000-82555600	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr15:82554000-82555600	Active TSS	Fetal Intestine Large	intestine
17	chr15:82554000-82555600	Active TSS	Right Atrium	heart
18	chr15:82554000-82555600	Active TSS	Stomach Smooth Muscle	stomach
19	chr15:82554000-82555600	Active TSS	HMEC	breast
20	chr15:82554000-82555600	Active TSS	HSMM	muscle
21	chr15:82554000-82555600	Active TSS	NHDF-Ad	bronchial
22	chr15:82554000-82555800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:82554000-82555800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:82554000-82555800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:82554000-82555800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:82554000-82555800	Active TSS	Fetal Intestine Small	intestine
27	chr15:82554000-82555800	Active TSS	K562	blood
28	chr15:82554000-82555800	Active TSS	NHLF	lung
29	chr15:82554000-82556000	Active TSS	H1 Cell Line	embryonic stem cell
30	chr15:82554000-82556000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:82554000-82556000	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr15:82554000-82556000	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr15:82554000-82556000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:82554000-82556000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:82554000-82556000	Active TSS	Brain Germinal Matrix	brain
36	chr15:82554000-82556000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr15:82554000-82556000	Active TSS	A549	lung
38	chr15:82554200-82555400	Active TSS	Duodenum Mucosa	Duodenum
39	chr15:82554200-82555400	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr15:82554200-82555400	Active TSS	Hela-S3	cervix
41	chr15:82554200-82555400	Active TSS	HepG2	liver
42	chr15:82554200-82555400	Active TSS	Osteobl	bone
43	chr15:82554200-82555600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:82554200-82555600	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr15:82554200-82555600	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr15:82554200-82555600	Active TSS	Muscle Satellite Cultured Cells	--
47	chr15:82554200-82555600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:82554200-82555600	Active TSS	Aorta	Aorta
49	chr15:82554200-82555600	Active TSS	Brain Anterior Caudate	brain
50	chr15:82554200-82555600	Active TSS	Pancreas	Pancrea

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