Variant report

Variant	rs1869301
Chromosome Location	chr15:40799568-40799569
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	HMGN3	chr15:40799256-40799700	K562	blood:	n/a	n/a
2	CTCF	chr15:40799235-40799640	IMR90	lung:	n/a	chr15:40799423-40799441
3	NANOG	chr15:40799205-40799631	H1-hESC	embryonic stem cell:	n/a	chr15:40799429-40799438
4	RAD21	chr15:40799128-40799763	HCT-116	colon:	n/a	chr15:40799572-40799582 chr15:40799421-40799440
5	CTCF	chr15:40799282-40799575	MCF-7	breast:	n/a	chr15:40799423-40799441
6	CTCF	chr15:40799292-40799581	ProgFib	skin:	n/a	chr15:40799423-40799441
7	CTCF	chr15:40799167-40799586	K562	blood:	n/a	chr15:40799423-40799441
8	ZNF143	chr15:40799270-40799581	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZBTB7A	chr15:40799094-40799685	ECC-1	luminal epithelium:	n/a	chr15:40799575-40799583
10	CTCF	chr15:40799157-40799716	MCF-7	breast:	n/a	chr15:40799423-40799441
11	CTCF	chr15:40799281-40799581	GM19238	blood:	n/a	chr15:40799423-40799441
12	POLR2A	chr15:40799194-40799594	K562	blood:	n/a	n/a
13	RAD21	chr15:40799193-40799578	A549	lung:	n/a	chr15:40799421-40799440
14	CTCF	chr15:40799295-40799579	GM19240	blood:	n/a	chr15:40799423-40799441
15	YY1	chr15:40799236-40799573	GM12878	blood:	n/a	n/a
16	RAD21	chr15:40799202-40799626	H1-hESC	embryonic stem cell:	n/a	chr15:40799572-40799582 chr15:40799421-40799440
17	RAD21	chr15:40799150-40799704	MCF-7	breast:	n/a	chr15:40799572-40799582 chr15:40799421-40799440
18	CTCF	chr15:40799242-40799605	A549	lung:	n/a	chr15:40799423-40799441
19	POLR2A	chr15:40799154-40799622	HCT-116	colon:	n/a	n/a
20	CTCF	chr15:40799228-40799571	T-47D	breast:	n/a	chr15:40799423-40799441
21	CTCF	chr15:40799279-40799571	MCF-7	breast:	n/a	chr15:40799423-40799441
22	POLR2A	chr15:40799137-40799695	K562	blood:	n/a	n/a
23	HEY1	chr15:40799189-40799637	K562	blood:	n/a	n/a
24	MAX	chr15:40799191-40799659	SK-N-SH	brain:	n/a	n/a
25	CTCF	chr15:40799420-40799570	HAc	cerebellar:	n/a	chr15:40799423-40799441
26	MAX	chr15:40799082-40799799	HCT-116	colon:	n/a	n/a
27	POLR2A	chr15:40799213-40799648	HCT-116	colon:	n/a	n/a
28	CTCF	chr15:40799420-40799570	WI-38	lung:	n/a	chr15:40799423-40799441
29	CTCF	chr15:40799420-40799570	HFF-Myc	foreskin:	n/a	chr15:40799423-40799441
30	CBX3	chr15:40799118-40799586	K562	blood:	n/a	n/a
31	MAX	chr15:40799212-40799629	K562	blood:	n/a	n/a
32	CTCF	chr15:40799316-40799569	GM19239	blood:	n/a	chr15:40799423-40799441
33	CTCF	chr15:40799199-40799605	A549	lung:	n/a	chr15:40799423-40799441
34	SIN3AK20	chr15:40799142-40799593	SK-N-SH	brain:	n/a	n/a
35	CTCF	chr15:40799283-40799588	MCF-7	breast:	n/a	chr15:40799423-40799441
36	CTCF	chr15:40799440-40799590	HA-sp	spinal cord:	n/a	n/a
37	JUND	chr15:40799173-40799576	K562	blood:	n/a	chr15:40799521-40799530 chr15:40799366-40799375
38	RAD21	chr15:40799245-40799659	H1-hESC	embryonic stem cell:	n/a	chr15:40799572-40799582 chr15:40799421-40799440
39	RAD21	chr15:40799137-40799725	A549	lung:	n/a	chr15:40799572-40799582 chr15:40799421-40799440
40	RAD21	chr15:40798984-40799791	HCT-116	colon:	n/a	chr15:40799572-40799582 chr15:40799421-40799440
41	POLR2A	chr15:40799151-40799599	K562	blood:	n/a	n/a
42	ZBTB7A	chr15:40799219-40799693	K562	blood:	n/a	chr15:40799575-40799583
43	RAD21	chr15:40799225-40799593	MCF-7	breast:	n/a	chr15:40799572-40799582 chr15:40799421-40799440
44	CTCF	chr15:40799224-40799792	K562	blood:	n/a	chr15:40799423-40799441
45	CTCF	chr15:40799231-40799645	GM12878	blood:	n/a	chr15:40799423-40799441
46	MAX	chr15:40799253-40799592	A549	lung:	n/a	n/a
47	POLR2A	chr15:40799185-40799615	K562	blood:	n/a	n/a
48	MYC	chr15:40799182-40799615	NB4	blood:	n/a	n/a
49	ELF1	chr15:40799240-40799698	GM12878	blood:	n/a	n/a
50	POLR2A	chr15:40799563-40799569	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40730539..40734458-chr15:40797952..40800684,3	K562	blood:
2	chr15:40761789..40767637-chr15:40797359..40801640,7	K562	blood:
3	chr15:40738741..40740672-chr15:40798310..40800042,2	K562	blood:
4	chr15:40769749..40770399-chr15:40799035..40799882,2	MCF-7	breast:
5	chr15:40714199..40714821-chr15:40799199..40799735,2	MCF-7	breast:
6	chr15:40731663..40736686-chr15:40795056..40800792,8	K562	blood:

Variant related genes	Relation type
ENSG00000259536	TF binding region
ENSG00000140320	Chromatin interaction
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11070275	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11070277	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11070285	0.96[CEU][hapmap]
rs11070286	0.96[CEU][hapmap]
rs11632061	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11632370	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11638742	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11639464	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11852694	0.96[CEU][hapmap]
rs11854986	0.96[CEU][hapmap]
rs11855334	0.96[CEU][hapmap]
rs11855923	0.96[CEU][hapmap]
rs11856438	0.96[CEU][hapmap]
rs11856802	1.00[CEU][hapmap]
rs11858113	0.96[CEU][hapmap]
rs12594548	1.00[CEU][hapmap];0.80[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12595610	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12905162	0.96[CEU][hapmap]
rs12914743	0.96[CEU][hapmap]
rs12916042	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16970851	0.96[CEU][hapmap]
rs1806961	0.87[EUR][1000 genomes]
rs1811513	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1813898	0.81[EUR][1000 genomes]
rs1869302	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1993212	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2034651	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2034652	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2167795	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2412531	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2412532	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2412534	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2412544	0.96[CEU][hapmap]
rs2444302	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2924386	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2924388	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2959536	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2959545	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3092979	0.96[CEU][hapmap]
rs35047458	0.96[CEU][hapmap]
rs3751653	0.96[CEU][hapmap]
rs4923875	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4923876	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4924472	0.96[CEU][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4924478	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924479	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924480	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924481	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs588686	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs590046	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs603623	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs616937	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs618399	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs619711	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs620198	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6492947	0.92[CEU][hapmap]
rs6492951	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs654317	0.82[EUR][1000 genomes]
rs6582	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7178756	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7183273	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7494968	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8026605	0.96[CEU][hapmap]
rs8029384	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs8034326	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs8041534	0.96[CEU][hapmap]
rs896795	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9652415	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs976401	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1869301	C15orf57	cis	Adipose Subcutaneous	GTEx
rs1869301	CCDC32	cis	lesional skin	skin_eQTL
rs1869301	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs1869301	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs1869301	C15orf57	cis	Muscle Skeletal	GTEx
rs1869301	C15orf57	cis	Nerve Tibial	GTEx
rs1869301	C15orf57	cis	lung	GTEx
rs1869301	CCDC32	cis	multi-tissue	Pritchard
rs1869301	C15orf57	cis	Artery Tibial	GTEx
rs1869301	CCDC32	cis	normal skin	skin_eQTL
rs1869301	C15orf57	cis	Cerebellum	GTEx
rs1869301	C15orf57	cis	Artery Aorta	GTEx
rs1869301	RP11-111A22.1	cis	Artery Tibial	GTEx
rs1869301	C15orf57	cis	Esophagus Muscularis	GTEx
rs1869301	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs1869301	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs1869301	RP11-111A22.1	cis	lung	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40798800-40799600	Enhancers	Fetal Heart	heart
2	chr15:40799000-40799600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr15:40799000-40799600	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr15:40799000-40799600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:40799000-40799600	Active TSS	Brain Anterior Caudate	brain
6	chr15:40799000-40799600	Flanking Active TSS	NHDF-Ad	bronchial
7	chr15:40799000-40799600	Active TSS	Osteobl	bone
8	chr15:40799000-40799800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr15:40799000-40799800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:40799000-40799800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:40799000-40799800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:40799000-40799800	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr15:40799000-40799800	Flanking Active TSS	Dnd41	blood
14	chr15:40799000-40799800	Flanking Active TSS	K562	blood
15	chr15:40799000-40799800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
16	chr15:40799200-40799600	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr15:40799200-40799600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
18	chr15:40799200-40799600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:40799200-40799600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
20	chr15:40799200-40799600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
21	chr15:40799200-40799600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:40799200-40799600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:40799200-40799600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:40799200-40799600	Flanking Active TSS	Liver	Liver
25	chr15:40799200-40799600	Flanking Active TSS	Brain Angular Gyrus	brain
26	chr15:40799200-40799600	Active TSS	Brain Germinal Matrix	brain
27	chr15:40799200-40799600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr15:40799200-40799600	Flanking Active TSS	Fetal Intestine Large	intestine
29	chr15:40799200-40799600	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr15:40799200-40799600	Flanking Active TSS	Placenta	Placenta
31	chr15:40799200-40799600	Flanking Active TSS	Fetal Stomach	stomach
32	chr15:40799200-40799600	Active TSS	Ovary	ovary
33	chr15:40799200-40799600	Flanking Active TSS	Pancreas	Pancrea
34	chr15:40799200-40799600	Active TSS	Psoas Muscle	Psoas
35	chr15:40799200-40799600	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr15:40799200-40799600	Flanking Active TSS	Right Atrium	heart
37	chr15:40799200-40799600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr15:40799200-40799600	Enhancers	Spleen	Spleen
39	chr15:40799200-40799600	Flanking Active TSS	NHEK	skin
40	chr15:40799200-40799800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:40799200-40799800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:40799200-40799800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
43	chr15:40799200-40799800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr15:40799200-40799800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:40799200-40799800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
46	chr15:40799200-40799800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
47	chr15:40799200-40799800	Bivalent Enhancer	Primary B cells from cord blood	blood
48	chr15:40799200-40799800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
49	chr15:40799200-40799800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:40799200-40799800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood

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