Variant report

Variant	rs1027230
Chromosome Location	chr15:40078863-40078864
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	CTCF	chr15:40078789-40078897	GM19239	blood:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
2	CTCF	chr15:40078740-40078890	HUVEC	blood vessel:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
3	SIN3A	chr15:40078750-40079014	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr15:40078741-40079049	A549	lung:	n/a	chr15:40078868-40078887 chr15:40078870-40078877
5	CTCF	chr15:40078760-40078910	GM12875	blood:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
6	CTCF	chr15:40078739-40078969	Gliobla	brain:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
7	CTCF	chr15:40078800-40078950	BE2_C	brain:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
8	MYC	chr15:40078812-40079034	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr15:40078720-40078870	HUVEC	blood vessel:	n/a	n/a
10	CTCF	chr15:40078780-40078930	GM12874	blood:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
11	CTCF	chr15:40078800-40078950	HCM	heart:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
12	CTCF	chr15:40078800-40078950	SK-N-SH_RA	brain:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
13	RAD21	chr15:40078662-40079074	MCF-7	breast:	n/a	chr15:40078868-40078887 chr15:40078870-40078877
14	CTCF	chr15:40078683-40079038	A549	lung:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
15	RAD21	chr15:40078761-40078986	K562	blood:	n/a	chr15:40078868-40078887 chr15:40078870-40078877
16	RAD21	chr15:40078582-40079123	A549	lung:	n/a	chr15:40078868-40078887 chr15:40078870-40078877
17	RAD21	chr15:40078698-40079045	GM12878	blood:	n/a	chr15:40078868-40078887 chr15:40078870-40078877
18	CTCF	chr15:40078840-40078990	GM12869	blood:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
19	CTCF	chr15:40078780-40078930	NHDF-neo	bronchial:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
20	IRF1	chr15:40078749-40079043	K562	blood:	n/a	chr15:40079033-40079043 chr15:40079029-40079043
21	CTCF	chr15:40078720-40078870	HRE	kidney:	n/a	n/a
22	CTCF	chr15:40078760-40078910	NB4	blood:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
23	CTCF	chr15:40078840-40078990	HCT-116	colon:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
24	RAD21	chr15:40078744-40079042	GM12878	blood:	n/a	chr15:40078868-40078887 chr15:40078870-40078877
25	CTCF	chr15:40078715-40078903	SK-N-SH_RA	brain:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
26	CTCF	chr15:40078741-40078903	GM19238	blood:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
27	RAD21	chr15:40078685-40079077	HepG2	liver:	n/a	chr15:40078868-40078887 chr15:40078870-40078877
28	CTCF	chr15:40078780-40078930	HCPEpiC	choroid plexus:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
29	RAD21	chr15:40078708-40078981	HepG2	liver:	n/a	chr15:40078868-40078887 chr15:40078870-40078877
30	CTCF	chr15:40078740-40078890	BE2_C	brain:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
31	CTCF	chr15:40078792-40078944	A549	lung:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
32	CTCF	chr15:40078760-40078910	GM12867	blood:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
33	CTCF	chr15:40078820-40078970	HAc	cerebellar:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
34	CTCF	chr15:40078800-40078950	GM12864	blood:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
35	RAD21	chr15:40078551-40079035	H1-hESC	embryonic stem cell:	n/a	chr15:40078868-40078887 chr15:40078870-40078877
36	CTCF	chr15:40078720-40078870	HA-sp	spinal cord:	n/a	n/a
37	CTCF	chr15:40078800-40078950	SAEC	small airway:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
38	CTCF	chr15:40078730-40079049	ECC-1	luminal epithelium:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
39	POLR2A	chr15:40078797-40078979	HUVEC	blood vessel:	n/a	n/a
40	HDAC2	chr15:40078799-40078958	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr15:40078800-40078950	HCPEpiC	choroid plexus:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
42	CTCF	chr15:40078800-40078950	HBMEC	blood vessel:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
43	CTCF	chr15:40078760-40078910	RPTEC	kidney:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
44	CTCF	chr15:40078780-40078930	GM12868	blood:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
45	CTCF	chr15:40078780-40078930	AoAF	blood vessel:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
46	CTCF	chr15:40078800-40078950	HMF	breast:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
47	CTCF	chr15:40078768-40078883	GM12891	blood:	n/a	chr15:40078872-40078880 chr15:40078870-40078883
48	CTCF	chr15:40078760-40078910	HFF-Myc	foreskin:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
49	CTCF	chr15:40078760-40078910	GM12869	blood:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
50	MYC	chr15:40078774-40078974	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:39877336..39879438-chr15:40075503..40079395,4	MCF-7	breast:
2	chr15:40078495..40079355-chr15:40566600..40567596,4	K562	blood:
3	chr15:40078363..40080929-chr15:40268662..40270401,2	MCF-7	breast:
4	chr15:40076890..40079993-chr15:40222713..40226528,3	K562	blood:
5	chr15:39873007..39875919-chr15:40078387..40080697,2	MCF-7	breast:
6	chr15:40074241..40077863-chr15:40078792..40081577,3	K562	blood:
7	chr15:40078779..40080616-chr15:40094906..40097630,2	MCF-7	breast:
8	chr15:40077135..40079271-chr15:40079393..40081898,2	MCF-7	breast:
9	chr15:40077399..40079202-chr15:40164859..40166897,2	MCF-7	breast:
10	chr15:40078638..40079472-chr15:40566591..40567310,2	MCF-7	breast:
11	chr15:40051644..40053868-chr15:40078451..40080226,2	MCF-7	breast:

Variant related genes	Relation type
FSIP1	TF binding region
ENSG00000128829	Chromatin interaction
ENSG00000261136	Chromatin interaction
ENSG00000150667	Chromatin interaction
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1027231	1.00[AFR][1000 genomes]
rs1166719	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1166720	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1166726	0.95[AFR][1000 genomes]
rs1688088	1.00[AFR][1000 genomes]
rs2631691	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2631716	1.00[AFR][1000 genomes]
rs2631719	1.00[AFR][1000 genomes]
rs2638008	1.00[AFR][1000 genomes]
rs2638011	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs589137	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs596717	1.00[AFR][1000 genomes]
rs603993	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs612775	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs621970	0.81[AFR][1000 genomes]
rs623984	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs628076	1.00[AFR][1000 genomes]
rs653964	0.95[AFR][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	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40075800-40079400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:40075800-40080600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:40076000-40079600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr15:40076000-40080600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr15:40076000-40081000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:40076000-40103200	Weak transcription	Right Atrium	heart
7	chr15:40076200-40079800	Weak transcription	Pancreas	Pancrea
8	chr15:40076200-40080000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:40076200-40080800	Weak transcription	Primary B cells from cord blood	blood
10	chr15:40076200-40081400	Weak transcription	Fetal Kidney	kidney
11	chr15:40076400-40079000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr15:40076400-40079200	Enhancers	Hela-S3	cervix
13	chr15:40076400-40080600	Weak transcription	Thymus	Thymus
14	chr15:40076600-40079000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:40076600-40079400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:40076600-40079800	Weak transcription	Fetal Thymus	thymus
17	chr15:40076600-40080000	Enhancers	HMEC	breast
18	chr15:40076600-40080200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:40076600-40080600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:40076600-40080600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:40076600-40081600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:40076600-40082000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:40076600-40082400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:40076600-40082600	Weak transcription	Primary T cells from cord blood	blood
25	chr15:40076600-40084200	Weak transcription	Adipose Nuclei	Adipose
26	chr15:40076600-40086200	Weak transcription	Fetal Muscle Leg	muscle
27	chr15:40076600-40090200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:40076600-40092600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:40076800-40082200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr15:40076800-40082400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:40077200-40079000	Enhancers	H1 Cell Line	embryonic stem cell
32	chr15:40077200-40079800	Weak transcription	HSMMtube	muscle
33	chr15:40077200-40081200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr15:40077200-40082600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:40077200-40082600	Enhancers	NHLF	lung
36	chr15:40077200-40092600	Weak transcription	NHEK	skin
37	chr15:40077200-40093200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:40077400-40079000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:40077400-40082600	Enhancers	Osteobl	bone
40	chr15:40077600-40079200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:40077600-40079800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:40077600-40082400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr15:40077600-40094600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:40077800-40079200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:40077800-40079600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr15:40077800-40080000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:40077800-40081200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:40077800-40082600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr15:40078000-40079600	Weak transcription	Fetal Lung	lung
50	chr15:40078000-40080600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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