Variant report

Variant	rs12442845
Chromosome Location	chr15:41049503-41049504
allele	A/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	USF1	chr15:41049156-41049536	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr15:41048960-41049711	SK-N-SH	brain:	n/a	chr15:41049373-41049382
3	MYC	chr15:41049193-41049578	NB4	blood:	n/a	chr15:41049383-41049393
4	EP300	chr15:41048686-41049984	SK-N-SH	brain:	n/a	n/a
5	MAX	chr15:41049121-41049599	SK-N-SH	brain:	n/a	chr15:41049383-41049393
6	TCF12	chr15:41048898-41049695	SK-N-SH	brain:	n/a	n/a
7	MXI1	chr15:41048685-41049870	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr15:41049117-41049526	MCF-7	breast:	n/a	chr15:41049373-41049382
9	EP300	chr15:41049020-41049675	SK-N-SH_RA	brain:	n/a	n/a
10	REST	chr15:41049116-41049584	SK-N-SH	brain:	n/a	n/a
11	RAD21	chr15:41049077-41049544	SK-N-SH_RA	brain:	n/a	n/a
12	GATA3	chr15:41048954-41049739	SK-N-SH	brain:	n/a	chr15:41049373-41049382
13	MAX	chr15:41049130-41049571	SK-N-SH	brain:	n/a	chr15:41049383-41049393
14	GATA3	chr15:41049085-41049653	MCF-7	breast:	n/a	chr15:41049373-41049382
15	GATA1	chr15:41049006-41049530	PBDE	blood:	n/a	chr15:41049373-41049382
16	RAD21	chr15:41049126-41049504	SK-N-SH_RA	brain:	n/a	n/a
17	BHLHE40	chr15:41049043-41049558	K562	blood:	n/a	n/a
18	EGR1	chr15:41049213-41049505	K562	blood:	n/a	n/a
19	USF1	chr15:41049188-41049507	SK-N-SH_RA	brain:	n/a	n/a
20	GATA2	chr15:41048994-41049779	SH-SY5Y	brain:	n/a	chr15:41049373-41049382
21	SIN3AK20	chr15:41048855-41049819	MCF-7	breast:	n/a	n/a
22	MAX	chr15:41049065-41049587	K562	blood:	n/a	chr15:41049383-41049393
23	GATA3	chr15:41049008-41049623	MCF-7	breast:	n/a	chr15:41049373-41049382
24	MYC	chr15:41049218-41049509	K562	blood:	n/a	chr15:41049383-41049393
25	USF1	chr15:41049217-41049575	K562	blood:	n/a	n/a
26	TEAD4	chr15:41049087-41049510	K562	blood:	n/a	n/a
27	MAX	chr15:41049075-41049575	NB4	blood:	n/a	chr15:41049383-41049393
28	GATA3	chr15:41049014-41049567	SH-SY5Y	brain:	n/a	chr15:41049373-41049382
29	HDAC2	chr15:41049103-41049514	MCF-7	breast:	n/a	n/a
30	POLR2A	chr15:41049107-41049546	SK-N-SH	brain:	n/a	n/a
31	MYC	chr15:41049178-41049509	MCF-7	breast:	n/a	chr15:41049383-41049393
32	EP300	chr15:41049046-41049659	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41046423..41049572-chr15:41185616..41187810,3	MCF-7	breast:
2	chr15:41047499..41049695-chr15:41052688..41055612,2	MCF-7	breast:
3	chr15:41042059..41049706-chr15:41053861..41061949,15	MCF-7	breast:
4	chr15:40984748..40990654-chr15:41044779..41050104,8	K562	blood:
5	chr15:41045896..41050408-chr15:41066208..41069896,5	MCF-7	breast:

Variant related genes	Relation type
RMDN3	TF binding region
SUMO2P15	TF binding region
ENSG00000104142	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000271236	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000245849	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	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631563	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[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];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11855560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858337	0.90[AFR][1000 genomes];0.95[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];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.95[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[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439683	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441514	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12593359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[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];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12912742	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2263551	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[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];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412548	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412549	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2577564	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2619679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619680	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2917955	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2928140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3092982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[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	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34400306	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36106105	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs45495293	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4923884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924493	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924495	0.91[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];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56042757	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492961	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7164339	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7167854	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]
rs7169010	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173646	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174551	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7175401	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs752012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025883	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033829	0.87[AMR][1000 genomes];0.88[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	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
4	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
5	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12442845	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs12442845	CCDC32	cis	multi-tissue	Pritchard
rs12442845	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12442845	RP11-111A22.1	cis	lung	GTEx
rs12442845	C15orf57	cis	Nerve Tibial	GTEx
rs12442845	C15orf57	cis	lung	GTEx
rs12442845	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12442845	C15orf57	cis	Artery Aorta	GTEx
rs12442845	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12442845	C15orf57	cis	Artery Tibial	GTEx
rs12442845	RAD51	cis	multi-tissue	Pritchard
rs12442845	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41048000-41049800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:41048000-41052200	Weak transcription	Thymus	Thymus
3	chr15:41048000-41055000	Weak transcription	Pancreas	Pancrea
4	chr15:41048000-41055200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:41048000-41055200	Weak transcription	Brain Substantia Nigra	brain
6	chr15:41048000-41055200	Weak transcription	NH-A	brain
7	chr15:41048000-41055400	Weak transcription	Brain Angular Gyrus	brain
8	chr15:41048000-41055400	Weak transcription	Right Atrium	heart
9	chr15:41048200-41049800	Enhancers	Primary hematopoietic stem cells	blood
10	chr15:41048200-41049800	Enhancers	Fetal Intestine Large	intestine
11	chr15:41048200-41050000	Enhancers	K562	blood
12	chr15:41048200-41050200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr15:41048200-41054600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:41048200-41055200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr15:41048200-41055200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:41048200-41055400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:41048200-41055400	Weak transcription	Liver	Liver
18	chr15:41048200-41055400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:41048200-41055400	Weak transcription	A549	lung
20	chr15:41048400-41049800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:41048400-41055000	Weak transcription	Lung	lung
22	chr15:41048400-41055000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:41048400-41055200	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:41048400-41055400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:41049200-41055200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:41049200-41055400	Weak transcription	GM12878-XiMat	blood
27	chr15:41049400-41049800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:41049400-41051200	Weak transcription	HepG2	liver
29	chr15:41049400-41052200	Weak transcription	Fetal Thymus	thymus
30	chr15:41049400-41054400	Weak transcription	Fetal Intestine Small	intestine
31	chr15:41049400-41054800	Weak transcription	Hela-S3	cervix

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