Variant report

Variant	rs11632640
Chromosome Location	chr15:41245289-41245290
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	CEBPB	chr15:41245255-41245652	HepG2	liver:	n/a	n/a
2	SP4	chr15:41244862-41246065	H1-hESC	embryonic stem cell:	n/a	chr15:41246045-41246061 chr15:41245611-41245627
3	ZKSCAN1	chr15:41244964-41245876	Hela-S3	cervix:	n/a	n/a
4	JUND	chr15:41245170-41245687	Hela-S3	cervix:	n/a	chr15:41245501-41245510
5	RFX5	chr15:41244826-41246079	SK-N-SH	brain:	n/a	chr15:41245500-41245509
6	CTCF	chr15:41245180-41245330	GM12870	blood:	n/a	n/a
7	POLR2A	chr15:41245224-41245858	K562	blood:	n/a	n/a
8	MAX	chr15:41244849-41246050	A549	lung:	n/a	chr15:41245041-41245050
9	KAP1	chr15:41245207-41245662	U2OS	brain:	n/a	n/a
10	EP300	chr15:41244980-41245986	ECC-1	luminal epithelium:	n/a	chr15:41245598-41245614
11	POLR2A	chr15:41245125-41245872	PFSK-1	brain:	n/a	n/a
12	CTCF	chr15:41245248-41245291	H1-hESC	embryonic stem cell:	n/a	n/a
13	MYC	chr15:41244811-41245706	H1-hESC	embryonic stem cell:	n/a	chr15:41245041-41245050
14	POLR2A	chr15:41245071-41246101	H1-neurons	neurons:	n/a	n/a
15	EBF1	chr15:41245051-41245841	GM12878	blood:	n/a	n/a
16	GTF2F1	chr15:41244675-41245972	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr15:41244982-41245830	HUVEC	blood vessel:	n/a	n/a
18	REST	chr15:41244829-41246248	H1-neurons	neurons:	n/a	chr15:41245517-41245530 chr15:41245604-41245617 chr15:41245601-41245614
19	TCF7L2	chr15:41244964-41245873	HCT-116	colon:	n/a	n/a
20	CEBPB	chr15:41245163-41245731	K562	blood:	n/a	n/a
21	MYC	chr15:41245114-41245739	K562	blood:	n/a	n/a
22	POLR2A	chr15:41244972-41245819	SK-N-SH	brain:	n/a	n/a
23	NFIC	chr15:41244945-41246078	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr15:41244087-41246309	MCF10A-Er-Src	breast:	n/a	n/a
25	CTCF	chr15:41245180-41245330	HEEpiC	esophagus:	n/a	n/a
26	MAX	chr15:41245038-41245800	K562	blood:	n/a	chr15:41245041-41245050
27	POLR2A	chr15:41244687-41246812	H1-hESC	embryonic stem cell:	n/a	n/a
28	FOXP2	chr15:41244864-41246113	PFSK-1	brain:	n/a	n/a
29	TAF7	chr15:41244820-41245496	H1-hESC	embryonic stem cell:	n/a	n/a
30	E2F6	chr15:41244676-41246153	H1-hESC	embryonic stem cell:	n/a	chr15:41245560-41245569 chr15:41244988-41244998 chr15:41245126-41245133 chr15:41245126-41245133 chr15:41245336-41245346 chr15:41245126-41245133
31	ELK1	chr15:41245026-41245837	Hela-S3	cervix:	n/a	n/a
32	RFX5	chr15:41244745-41245828	Hela-S3	cervix:	n/a	chr15:41245500-41245509
33	MAZ	chr15:41244802-41245909	K562	blood:	n/a	chr15:41245041-41245050
34	POLR2A	chr15:41244960-41245966	MCF-7	breast:	n/a	n/a
35	POLR2A	chr15:41244901-41245868	A549	lung:	n/a	n/a
36	POLR2A	chr15:41244822-41246504	PBDE	blood:	n/a	n/a
37	POLR2A	chr15:41244697-41246315	GM19193	blood:	n/a	n/a
38	CEBPB	chr15:41245003-41245771	IMR90	lung:	n/a	n/a
39	POLR2A	chr15:41244452-41246039	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr15:41244981-41245961	SK-N-MC	brain:	n/a	n/a
41	POLR2A	chr15:41244700-41245945	MCF-7	breast:	n/a	n/a
42	PBX3	chr15:41245240-41245851	A549	lung:	n/a	chr15:41245559-41245568 chr15:41245500-41245509
43	STAT5A	chr15:41245017-41245497	GM12878	blood:	n/a	n/a
44	EP300	chr15:41245227-41245721	K562	blood:	n/a	chr15:41245598-41245614
45	POLR2A	chr15:41244823-41245521	A549	lung:	n/a	n/a
46	CTCF	chr15:41245180-41245330	GM12872	blood:	n/a	n/a
47	CEBPB	chr15:41245278-41245617	HepG2	liver:	n/a	n/a
48	SMARCC1	chr15:41244649-41246206	Hela-S3	cervix:	n/a	n/a
49	TBP	chr15:41244635-41246113	H1-hESC	embryonic stem cell:	n/a	n/a
50	MXI1	chr15:41244826-41245720	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41245148..41245725-chr17:75277480..75278058,2	Hela-S3	cervix:
2	chr15:41243575..41247241-chr15:41275161..41277167,3	MCF-7	breast:
3	chr15:41219948..41223850-chr15:41241031..41249080,13	K562	blood:
4	chr15:41244983..41245699-chr17:62222870..62223655,2	Hela-S3	cervix:
5	chr15:41196932..41200984-chr15:41244050..41248455,6	K562	blood:
6	chr15:41244727..41245305-chr9:91933111..91933989,2	Hela-S3	cervix:
7	chr15:41046641..41048842-chr15:41243931..41246219,2	K562	blood:
8	chr15:41220084..41222525-chr15:41245007..41247668,2	MCF-7	breast:
9	chr15:41219573..41224863-chr15:41243808..41249661,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHAC1-1	chr15:41244582-41245400	XLOC_011224

Variant related genes	Relation type
CHAC1	TF binding region
ISCA1P4	TF binding region
ENSG00000128917	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000184640	Chromatin interaction
ENSG00000263718	Chromatin interaction
ENSG00000266402	Chromatin interaction
ENSG00000187742	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11070312	0.90[ASN][1000 genomes]
rs11634736	0.93[ASN][1000 genomes]
rs4924519	0.86[ASN][1000 genomes]
rs7175269	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv904106	chr15:41221067-41259523	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	esv1794127	chr15:41245289-41276158	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41244200-41246200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:41244400-41245400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:41244400-41245400	Flanking Active TSS	Pancreas	Pancrea
4	chr15:41244400-41245400	Flanking Active TSS	HMEC	breast
5	chr15:41244400-41246200	Active TSS	A549	lung
6	chr15:41244400-41246600	Active TSS	Brain Angular Gyrus	brain
7	chr15:41244400-41246800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:41244400-41246800	Active TSS	Rectal Smooth Muscle	rectum
9	chr15:41244600-41245400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:41244600-41245600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:41244600-41246000	Enhancers	Fetal Brain Male	brain
12	chr15:41244600-41246000	Active TSS	Osteobl	bone
13	chr15:41244600-41246200	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr15:41244600-41246200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr15:41244600-41246200	Active TSS	HSMM	muscle
16	chr15:41244600-41246200	Active TSS	NHLF	lung
17	chr15:41244600-41246400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:41244600-41246400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:41244600-41246400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:41244600-41246400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr15:41244600-41246400	Flanking Active TSS	Liver	Liver
22	chr15:41244600-41246400	Flanking Active TSS	Colonic Mucosa	Colon
23	chr15:41244600-41246600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:41244600-41246800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr15:41244600-41246800	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr15:41244600-41247200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:41244800-41245400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:41244800-41245400	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr15:41244800-41245400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
30	chr15:41244800-41245400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
31	chr15:41244800-41245400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr15:41244800-41245400	Flanking Active TSS	Thymus	Thymus
33	chr15:41244800-41246000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:41244800-41246000	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr15:41244800-41246000	Flanking Active TSS	Fetal Thymus	thymus
36	chr15:41244800-41246200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:41244800-41246200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:41244800-41246200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr15:41244800-41246200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:41244800-41246200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:41244800-41246200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:41244800-41246200	Active TSS	Psoas Muscle	Psoas
43	chr15:41244800-41246200	Active TSS	Small Intestine	intestine
44	chr15:41244800-41246400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:41244800-41246400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:41244800-41246400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
47	chr15:41244800-41246600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr15:41244800-41246600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:41244800-41246600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr15:41244800-41246600	Active TSS	Brain Substantia Nigra	brain

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