Variant report

Variant	rs2162246
Chromosome Location	chr15:45461401-45461402
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	EP300	chr15:45461397-45462508	SK-N-SH_RA	brain:	n/a	n/a
2	MAX	chr15:45461290-45461851	K562	blood:	n/a	chr15:45461631-45461641
3	NR2F2	chr15:45461198-45461955	K562	blood:	n/a	n/a
4	EP300	chr15:45460616-45462717	SK-N-SH	brain:	n/a	chr15:45460666-45460682
5	POLR2A	chr15:45461269-45461907	K562	blood:	n/a	n/a
6	GATA1	chr15:45461238-45461953	PBDE	blood:	n/a	chr15:45461404-45461421 chr15:45461402-45461412 chr15:45461645-45461662 chr15:45461399-45461415
7	CBX3	chr15:45461391-45461823	K562	blood:	n/a	n/a
8	TBL1XR1	chr15:45461008-45461685	K562	blood:	n/a	n/a
9	TCF12	chr15:45461345-45462438	SK-N-SH	brain:	n/a	chr15:45462058-45462068
10	TAL1	chr15:45461375-45461931	K562	blood:	n/a	chr15:45461403-45461421 chr15:45461637-45461652 chr15:45461645-45461663
11	MAZ	chr15:45461258-45461800	K562	blood:	n/a	chr15:45461631-45461641
12	POLR2A	chr15:45461018-45462010	K562	blood:	n/a	n/a
13	GATA2	chr15:45461231-45462493	SH-SY5Y	brain:	n/a	chr15:45461404-45461421 chr15:45461402-45461412 chr15:45461645-45461662 chr15:45461399-45461415
14	RCOR1	chr15:45461325-45461777	K562	blood:	n/a	n/a
15	RCOR1	chr15:45461170-45461752	K562	blood:	n/a	n/a
16	POLR2A	chr15:45461387-45461882	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45459427..45462384-chr15:45693635..45696116,3	K562	blood:
2	chr15:45459774..45461695-chr15:45467150..45468709,2	K562	blood:
3	chr15:45458146..45462463-chr15:45465556..45468797,6	MCF-7	breast:
4	chr15:45459519..45461778-chr15:45469004..45470564,2	K562	blood:
5	chr15:45458776..45462841-chr15:45467209..45473486,10	K562	blood:
6	chr15:45459071..45462844-chr15:45693635..45696532,4	K562	blood:
7	chr15:45458639..45462602-chr15:45463163..45466877,10	K562	blood:
8	chr15:45458639..45463256-chr15:45489443..45493548,9	K562	blood:
9	chr15:45444706..45447350-chr15:45459510..45461724,2	K562	blood:
10	chr15:45457999..45463256-chr15:45488727..45493013,8	K562	blood:
11	chr15:45457610..45461525-chr15:45477333..45480560,5	MCF-7	breast:
12	chr15:45457346..45461990-chr15:45488766..45494297,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259519	TF binding region
ENSG00000259539	TF binding region
ENSG00000138606	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000259932	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000260035	Chromatin interaction
ENSG00000137857	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1145089	1.00[JPT][hapmap]
rs1620253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648307	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648310	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648313	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706807	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706811	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706812	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706815	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1706817	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706827	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs1706829	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes]
rs2292468	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs2458237	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467819	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467820	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775830	0.80[AMR][1000 genomes]
rs6493143	1.00[JPT][hapmap]
rs7169193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
6	nsv518213	chr15:45421758-45464768	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2162246	ADAL	cis	parietal	SCAN
rs2162246	SHF	cis	cerebellum	SCAN
rs2162246	SHF	cis	parietal	SCAN
rs2162246	CCNDBP1	cis	cerebellum	SCAN
rs2162246	FSIP1	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45459600-45461800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:45459600-45463800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:45459600-45469200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:45459800-45461800	Enhancers	Spleen	Spleen
5	chr15:45459800-45462200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:45459800-45462400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr15:45459800-45462400	Enhancers	Primary B cells from peripheral blood	blood
8	chr15:45459800-45463200	Weak transcription	Ovary	ovary
9	chr15:45459800-45471800	Weak transcription	Small Intestine	intestine
10	chr15:45459800-45478000	Weak transcription	Aorta	Aorta
11	chr15:45460000-45461600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:45460000-45461800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:45460000-45461800	Weak transcription	GM12878-XiMat	blood
14	chr15:45460000-45462000	Weak transcription	Primary B cells from cord blood	blood
15	chr15:45460000-45462000	Weak transcription	HSMM	muscle
16	chr15:45460000-45462200	Enhancers	Brain Hippocampus Middle	brain
17	chr15:45460000-45462400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr15:45460000-45462400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:45460000-45462400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:45460000-45462400	Enhancers	Primary hematopoietic stem cells	blood
21	chr15:45460000-45462400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr15:45460000-45462600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr15:45460000-45463800	Weak transcription	Right Ventricle	heart
24	chr15:45460000-45465000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:45460000-45465600	Weak transcription	Fetal Intestine Large	intestine
26	chr15:45460000-45465600	Weak transcription	HSMMtube	muscle
27	chr15:45460000-45466600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:45460000-45471600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:45460000-45471800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:45460000-45472200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:45460000-45474800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:45460000-45477200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:45460000-45478600	Weak transcription	Thymus	Thymus
34	chr15:45460200-45461600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:45460200-45461800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:45460200-45461800	Genic enhancers	Fetal Stomach	stomach
37	chr15:45460200-45462000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:45460200-45462200	Enhancers	Fetal Muscle Trunk	muscle
39	chr15:45460200-45462400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:45460200-45462600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr15:45460200-45462600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:45460200-45462800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:45460200-45463200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:45460200-45463200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr15:45460200-45463200	Weak transcription	HepG2	liver
46	chr15:45460200-45463600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:45460200-45463800	Weak transcription	Colonic Mucosa	Colon
48	chr15:45460200-45464400	Weak transcription	Colon Smooth Muscle	Colon
49	chr15:45460200-45467000	Strong transcription	Fetal Intestine Small	intestine
50	chr15:45460200-45478000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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