Variant report

Variant	rs16972973
Chromosome Location	chr15:42567158-42567159
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	WRNIP1	chr15:42564953-42567418	GM12878	blood:	n/a	n/a
2	MYC	chr15:42567117-42567316	MCF10A-Er-Src	breast:	n/a	chr15:42567154-42567161
3	GTF3C2	chr15:42565855-42567301	Hela-S3	cervix:	n/a	n/a
4	HCFC1	chr15:42564125-42567794	Hela-S3	cervix:	n/a	n/a
5	TBP	chr15:42564199-42567248	Hela-S3	cervix:	n/a	n/a
6	GTF3C2	chr15:42566783-42567604	K562	blood:	n/a	n/a
7	MAX	chr15:42565143-42567875	NB4	blood:	n/a	chr15:42567154-42567161
8	POLR2A	chr15:42567014-42567171	HepG2	liver:	n/a	n/a
9	UBTF	chr15:42565085-42567159	K562	blood:	n/a	n/a
10	RPC155	chr15:42566765-42567302	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr15:42564068-42568476	SK-N-SH	brain:	n/a	n/a
12	EP300	chr15:42566992-42567180	HepG2	liver:	n/a	n/a
13	POLR2A	chr15:42565014-42567783	HepG2	liver:	n/a	n/a
14	BHLHE40	chr15:42565191-42567220	K562	blood:	n/a	n/a
15	POLR2A	chr15:42564854-42567158	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42453296..42455922-chr15:42565346..42568176,2	K562	blood:
2	chr15:42565305..42567163-chr15:42839364..42842481,3	K562	blood:
3	chr15:42498938..42502268-chr15:42564432..42567193,3	MCF-7	breast:

Variant related genes	Relation type
TMEM87A	TF binding region
GANC	TF binding region
ENSG00000137814	Chromatin interaction
ENSG00000166887	Chromatin interaction
ENSG00000261002	Chromatin interaction
ENSG00000180979	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs16972704	1.00[EUR][1000 genomes]
rs16972772	1.00[EUR][1000 genomes]
rs16972775	1.00[EUR][1000 genomes]
rs16972983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16972993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973103	1.00[EUR][1000 genomes]
rs16973149	1.00[EUR][1000 genomes]
rs16973183	1.00[EUR][1000 genomes]
rs16973203	1.00[EUR][1000 genomes]
rs16973233	1.00[EUR][1000 genomes]
rs28364353	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364361	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364362	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364364	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364366	1.00[AMR][1000 genomes]
rs28364375	1.00[EUR][1000 genomes]
rs28364412	1.00[EUR][1000 genomes]
rs28364442	1.00[EUR][1000 genomes]
rs28364445	1.00[EUR][1000 genomes]
rs28364450	1.00[EUR][1000 genomes]
rs28364499	1.00[EUR][1000 genomes]
rs59897576	1.00[EUR][1000 genomes]
rs61735534	1.00[EUR][1000 genomes]
rs6493032	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7163294	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7164282	1.00[EUR][1000 genomes]
rs7183741	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8026177	1.00[EUR][1000 genomes]
rs8031541	1.00[EUR][1000 genomes]
rs8037390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8037485	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8037624	1.00[EUR][1000 genomes]
rs8041155	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042890	1.00[AMR][1000 genomes]
rs9672364	1.00[EUR][1000 genomes]
rs9745221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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	73 gene(s)	inside rSNPs	diseases
5	esv1807328	chr15:42525300-42573278	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 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	chr15:42563200-42567400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr15:42563400-42568200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:42563400-42568600	Active TSS	Right Atrium	heart
4	chr15:42564000-42567200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:42564000-42567600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr15:42564000-42568400	Active TSS	K562	blood
7	chr15:42564400-42567800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr15:42564400-42568400	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr15:42564400-42568400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:42564600-42567600	Active TSS	Esophagus	oesophagus
11	chr15:42564600-42567600	Active TSS	Lung	lung
12	chr15:42564600-42567600	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr15:42564600-42567800	Bivalent/Poised TSS	HepG2	liver
14	chr15:42564600-42568000	Active TSS	Right Ventricle	heart
15	chr15:42564600-42568400	Active TSS	Aorta	Aorta
16	chr15:42564600-42568400	Active TSS	Ovary	ovary
17	chr15:42564800-42568200	Active TSS	Colonic Mucosa	Colon
18	chr15:42565000-42567200	Active TSS	Gastric	stomach
19	chr15:42565800-42567200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr15:42565800-42567200	Flanking Active TSS	NH-A	brain
21	chr15:42565800-42567800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr15:42565800-42568400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr15:42565800-42568400	Flanking Active TSS	HUVEC	blood vessel
24	chr15:42565800-42568600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:42565800-42568600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr15:42565800-42568600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr15:42566000-42567200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr15:42566000-42567400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr15:42566000-42567800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr15:42566000-42567800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:42566000-42567800	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr15:42566000-42568400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:42566000-42568600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:42566000-42568600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr15:42566000-42568800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:42566200-42567400	Flanking Active TSS	Fetal Brain Female	brain
37	chr15:42566400-42567400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr15:42566400-42567400	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr15:42566400-42567800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:42566400-42568000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr15:42566400-42568200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr15:42566400-42576000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:42566600-42567200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr15:42566600-42567200	Flanking Active TSS	Fetal Stomach	stomach
45	chr15:42566600-42567200	Flanking Active TSS	NHEK	skin
46	chr15:42566600-42567400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr15:42566600-42567400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr15:42566600-42567400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr15:42566600-42567400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:42566600-42567400	Flanking Active TSS	Brain Cingulate Gyrus	brain

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