Variant report

Variant	rs1867419
Chromosome Location	chr15:41806219-41806220
allele	C/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	MAX	chr15:41805835-41806649	ECC-1	luminal epithelium:	n/a	n/a
2	PAX5	chr15:41806217-41806466	GM12878	blood:	n/a	chr15:41806237-41806246
3	POLR2A	chr15:41806210-41806371	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr15:41805811-41806431	NB4	blood:	n/a	n/a
5	ZMIZ1	chr15:41805781-41806324	K562	blood:	n/a	n/a
6	MYC	chr15:41805393-41806508	K562	blood:	n/a	n/a
7	KAP1	chr15:41805690-41806481	HEK293	kidney:	n/a	n/a
8	MYC	chr15:41805377-41806468	K562	blood:	n/a	n/a
9	JUND	chr15:41805734-41806470	K562	blood:	n/a	chr15:41806353-41806361
10	TEAD4	chr15:41805173-41806530	K562	blood:	n/a	n/a
11	GABPA	chr15:41805790-41806256	K562	blood:	n/a	n/a
12	ZBTB7A	chr15:41805688-41806259	K562	blood:	n/a	n/a
13	POLR2A	chr15:41805887-41806709	K562	blood:	n/a	n/a
14	POLR2A	chr15:41805303-41806510	K562	blood:	n/a	n/a
15	HEY1	chr15:41805780-41806313	K562	blood:	n/a	chr15:41806109-41806124
16	ELF1	chr15:41805809-41806390	GM12878	blood:	n/a	chr15:41806136-41806145 chr15:41806135-41806144
17	ZNF143	chr15:41805776-41806255	K562	blood:	n/a	chr15:41806204-41806222 chr15:41806074-41806092
18	TBL1XR1	chr15:41805813-41806249	K562	blood:	n/a	n/a
19	TCF7L2	chr15:41805691-41806647	HCT-116	colon:	n/a	n/a
20	HCFC1	chr15:41805354-41806338	K562	blood:	n/a	n/a
21	MAX	chr15:41805768-41806491	K562	blood:	n/a	n/a
22	MAZ	chr15:41806095-41806244	GM12878	blood:	n/a	n/a
23	HEY1	chr15:41806095-41806425	K562	blood:	n/a	chr15:41806109-41806124
24	RUNX3	chr15:41806168-41806531	GM12878	blood:	n/a	n/a
25	TBP	chr15:41805850-41806538	K562	blood:	n/a	n/a
26	POLR2A	chr15:41805611-41806586	K562	blood:	n/a	n/a
27	RUNX3	chr15:41806185-41806513	GM12878	blood:	n/a	n/a
28	MAX	chr15:41806165-41806400	GM12878	blood:	n/a	n/a
29	IRF1	chr15:41805885-41806352	K562	blood:	n/a	chr15:41806062-41806076
30	RCOR1	chr15:41805255-41806232	K562	blood:	n/a	n/a
31	UBTF	chr15:41805206-41806318	K562	blood:	n/a	n/a
32	CBX3	chr15:41805542-41806445	K562	blood:	n/a	n/a
33	POLR2A	chr15:41805554-41806284	Gliobla	brain:	n/a	n/a
34	HMGN3	chr15:41804926-41806286	K562	blood:	n/a	n/a
35	POLR2A	chr15:41805803-41806412	HCT-116	colon:	n/a	n/a
36	CTBP2	chr15:41805373-41806435	H1-hESC	embryonic stem cell:	n/a	n/a
37	ELF1	chr15:41805776-41806345	K562	blood:	n/a	chr15:41806136-41806145 chr15:41806135-41806144
38	JUN	chr15:41805585-41806855	K562	blood:	n/a	chr15:41806353-41806361 chr15:41806837-41806846
39	POLR2A	chr15:41805842-41806432	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr15:41805905-41806517	Hela-S3	cervix:	n/a	n/a
41	MAX	chr15:41805215-41806568	K562	blood:	n/a	n/a
42	POLR2A	chr15:41805910-41806404	ECC-1	luminal epithelium:	n/a	n/a
43	RCOR1	chr15:41805259-41806402	K562	blood:	n/a	n/a
44	TCF7L2	chr15:41805909-41806515	HEK293	kidney:	n/a	n/a
45	POLR2A	chr15:41805808-41806391	HCT-116	colon:	n/a	n/a
46	POLR2A	chr15:41805677-41806627	K562	blood:	n/a	n/a
47	GABPA	chr15:41805555-41806427	K562	blood:	n/a	n/a
48	ZNF263	chr15:41805694-41806550	HEK293-T-REx	kidney:	n/a	chr15:41806093-41806114
49	SIN3AK20	chr15:41805736-41806259	K562	blood:	n/a	n/a
50	MAX	chr15:41805775-41806542	K562	blood:	n/a	n/a

Variant related genes	Relation type
LTK	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1077809	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10851405	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070331	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200340	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2253936	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289740	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2297377	0.84[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2297378	0.80[CHB][hapmap]
rs2777490	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316622	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs316623	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3759793	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8035331	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8035575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv471241	chr15:41783814-41820200	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1867419	RPAP1	cis	multi-tissue	Pritchard
rs1867419	LTK	cis	lung	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41801800-41819000	Weak transcription	Hela-S3	cervix
2	chr15:41803200-41806400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr15:41803200-41806400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:41803400-41806400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr15:41803600-41806400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:41803800-41806400	Bivalent Enhancer	Fetal Thymus	thymus
7	chr15:41804000-41806400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:41804000-41806400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:41804000-41806400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
10	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
11	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
12	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
13	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
15	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
16	chr15:41804400-41806400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:41804400-41806400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
18	chr15:41804400-41806400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr15:41804400-41806400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
20	chr15:41804400-41806400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
21	chr15:41804400-41806400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr15:41804400-41806400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
23	chr15:41804400-41806400	Flanking Active TSS	Right Ventricle	heart
24	chr15:41804400-41806600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:41804600-41806400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr15:41804800-41806400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr15:41804800-41806400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:41804800-41806400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
29	chr15:41805000-41806400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
30	chr15:41805200-41806400	Enhancers	HSMMtube	muscle
31	chr15:41805200-41809200	Weak transcription	A549	lung
32	chr15:41805400-41806400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr15:41805400-41806600	Bivalent Enhancer	Liver	Liver
34	chr15:41805600-41806400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr15:41805600-41806400	Bivalent/Poised TSS	Fetal Kidney	kidney
36	chr15:41805600-41806400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr15:41805800-41806400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
38	chr15:41805800-41806400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr15:41805800-41806400	Bivalent Enhancer	NHEK	skin
40	chr15:41805800-41806600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
41	chr15:41805800-41806600	Enhancers	Spleen	Spleen
42	chr15:41805800-41806600	Flanking Active TSS	GM12878-XiMat	blood
43	chr15:41806000-41806400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:41806000-41806400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:41806000-41806400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:41806000-41806400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:41806000-41806400	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:41806000-41806400	Flanking Active TSS	Colonic Mucosa	Colon
49	chr15:41806000-41806400	Enhancers	Esophagus	oesophagus
50	chr15:41806000-41806400	Bivalent Enhancer	Psoas Muscle	Psoas

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