Variant report

Variant	rs3844075
Chromosome Location	chr15:44068160-44068161
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	RELA	chr15:44068078-44068815	GM19099	blood:	n/a	n/a
2	POLR2A	chr15:44067881-44068296	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr15:44066458-44068341	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr15:44067369-44068597	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr15:44065857-44068466	PFSK-1	brain:	n/a	n/a
6	KAP1	chr15:44067630-44068636	HEK293	kidney:	n/a	n/a
7	POLR2A	chr15:44067575-44069189	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr15:44067544-44070106	GM12892	blood:	n/a	n/a
9	ZEB1	chr15:44068151-44068933	GM12878	blood:	n/a	chr15:44068470-44068482 chr15:44068229-44068242
10	POLR2A	chr15:44064991-44070109	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:44064546-44069220	GM12878	blood:	n/a	n/a
12	RUNX3	chr15:44068099-44070145	GM12878	blood:	n/a	chr15:44069713-44069730
13	POLR2A	chr15:44067495-44068859	Hela-S3	cervix:	n/a	n/a
14	PAX5	chr15:44068072-44068984	GM12878	blood:	n/a	n/a
15	TCF3	chr15:44068098-44068867	GM12878	blood:	n/a	n/a
16	STAT5A	chr15:44067733-44069918	GM12878	blood:	n/a	chr15:44068876-44068888
17	EBF1	chr15:44067585-44069985	GM12878	blood:	n/a	chr15:44068925-44068935 chr15:44068495-44068506 chr15:44068534-44068545 chr15:44067839-44067848 chr15:44068924-44068937 chr15:44068926-44068935
18	MTA3	chr15:44067495-44070163	GM12878	blood:	n/a	n/a
19	SIN3A	chr15:44067607-44070030	H1-hESC	embryonic stem cell:	n/a	chr15:44069898-44069907
20	POLR2A	chr15:44063327-44069078	K562	blood:	n/a	n/a
21	MAX	chr15:44067454-44068175	HepG2	liver:	n/a	chr15:44067738-44067748
22	POLR2A	chr15:44067319-44070009	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr15:44067655-44070003	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:44067531-44070019	HepG2	liver:	n/a	n/a
25	RELA	chr15:44068075-44069949	GM18951	blood:	n/a	n/a
26	EBF1	chr15:44068141-44070065	GM12878	blood:	n/a	chr15:44068925-44068935 chr15:44068495-44068506 chr15:44068534-44068545 chr15:44068924-44068937 chr15:44068926-44068935
27	POLR2A	chr15:44068133-44070027	GM12878	blood:	n/a	n/a
28	CTCF	chr15:44067579-44068266	HCT-116	colon:	n/a	n/a
29	POLR2A	chr15:44067601-44070073	GM18505	blood:	n/a	n/a
30	POLR2A	chr15:44067589-44070055	GM19193	blood:	n/a	n/a
31	POLR2A	chr15:44066024-44070065	GM12891	blood:	n/a	n/a
32	HCFC1	chr15:44066076-44070249	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr15:44067449-44070081	MCF-7	breast:	n/a	n/a
34	POLR2A	chr15:44066121-44069686	A549	lung:	n/a	n/a
35	POLR2A	chr15:44067678-44070045	GM15510	blood:	n/a	n/a
36	POLR2A	chr15:44067768-44070087	Raji	blood:	n/a	n/a
37	YY1	chr15:44067907-44068175	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr15:44068102-44069776	GM12878	blood:	n/a	n/a
39	MTA3	chr15:44067613-44068914	GM12878	blood:	n/a	n/a
40	POLR2A	chr15:44067484-44068935	K562	blood:	n/a	n/a
41	POLR2A	chr15:44067627-44068824	HL-60	blood:	n/a	n/a
42	POLR2A	chr15:44066283-44070080	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr15:44068141-44069969	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr15:44068154-44068598	K562	blood:	n/a	n/a
45	POLR2A	chr15:44066175-44068637	U87	brain:	n/a	n/a
46	POLR2A	chr15:44067515-44069216	GM12891	blood:	n/a	n/a
47	POLR2A	chr15:44068090-44068826	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr15:44067753-44070020	GM18526	blood:	n/a	n/a
49	POLR2A	chr15:44067464-44070063	GM12892	blood:	n/a	n/a
50	POLR2A	chr15:44066224-44068637	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:44066200..44071612-chr15:44082403..44086035,7	K562	blood:
2	chr15:44066929..44069824-chr15:44091677..44094250,3	K562	blood:
3	chr15:44060010..44065607-chr15:44066577..44070669,7	K562	blood:
4	chr15:44067949..44070096-chr15:44073710..44075913,2	MCF-7	breast:
5	chr15:44061265..44064131-chr15:44066362..44068342,4	K562	blood:
6	chr15:44065408..44074556-chr15:44080543..44088380,28	MCF-7	breast:
7	chr15:44062113..44074982-chr15:44088756..44097846,29	MCF-7	breast:
8	chr15:44036049..44038671-chr15:44067430..44069245,2	K562	blood:
9	chr15:44065227..44073214-chr15:44081584..44094479,46	MCF-7	breast:
10	chr15:44067455..44069837-chr15:44100088..44102912,2	MCF-7	breast:
11	chr15:44067854..44069742-chr15:44115622..44117150,2	MCF-7	breast:
12	chr15:44060550..44065898-chr15:44066868..44071265,7	MCF-7	breast:
13	chr15:44068154..44070774-chr15:44115060..44118766,3	K562	blood:

Variant related genes	Relation type
ELL3	TF binding region
SERF2	TF binding region
ENSG00000167004	Chromatin interaction
ENSG00000140259	Chromatin interaction
ENSG00000242028	Chromatin interaction
ENSG00000184716	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000205771	Chromatin interaction
ENSG00000268488	Chromatin interaction
ENSG00000221792	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10163069	0.85[YRI][hapmap];0.92[AFR][1000 genomes]
rs12443084	1.00[YRI][hapmap]
rs2930530	0.96[YRI][hapmap]
rs3986209	0.87[AFR][1000 genomes]
rs4923964	0.82[AFR][1000 genomes]
rs7178230	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
9	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
10	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44041000-44068800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:44044400-44068200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:44057600-44068200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:44059200-44068600	Weak transcription	Small Intestine	intestine
5	chr15:44062400-44068600	Weak transcription	Fetal Heart	heart
6	chr15:44062800-44068600	Weak transcription	Fetal Brain Male	brain
7	chr15:44064000-44068200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:44064200-44068600	Weak transcription	Right Atrium	heart
9	chr15:44064400-44068200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr15:44064400-44068600	Weak transcription	Brain Substantia Nigra	brain
11	chr15:44064400-44068800	Weak transcription	Aorta	Aorta
12	chr15:44064400-44068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:44064400-44068800	Weak transcription	Ovary	ovary
14	chr15:44064800-44068400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:44064800-44068600	Weak transcription	Psoas Muscle	Psoas
16	chr15:44065000-44068600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:44065200-44068200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr15:44065200-44068200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:44065200-44068200	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:44065400-44068400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:44065400-44068400	Weak transcription	Fetal Kidney	kidney
22	chr15:44065400-44068400	Weak transcription	NHDF-Ad	bronchial
23	chr15:44065400-44068600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr15:44065400-44068600	Weak transcription	Brain Angular Gyrus	brain
25	chr15:44065400-44068600	Weak transcription	NHLF	lung
26	chr15:44065600-44068200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:44065600-44068400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:44065600-44068400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr15:44065600-44068400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr15:44065600-44068600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr15:44065600-44068600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr15:44065600-44068600	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:44065600-44068600	Weak transcription	HUVEC	blood vessel
34	chr15:44065800-44068200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:44065800-44068200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:44065800-44068400	Weak transcription	Thymus	Thymus
37	chr15:44066000-44068200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr15:44066400-44068200	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr15:44066400-44068200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:44066400-44068200	Weak transcription	K562	blood
41	chr15:44066400-44068400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:44066400-44068400	Weak transcription	Adipose Nuclei	Adipose
43	chr15:44066400-44068600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:44066400-44069400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:44066600-44068200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:44066600-44068200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:44066600-44068200	Weak transcription	Primary T cells from cord blood	blood
48	chr15:44066600-44068200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:44066600-44068200	Weak transcription	Fetal Muscle Leg	muscle
50	chr15:44066600-44068200	Weak transcription	Gastric	stomach

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