Variant report

Variant	rs1860509
Chromosome Location	chr7:139478175-139478176
allele	A/C
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	MAX	chr7:139477731-139478708	SK-N-SH	brain:	n/a	n/a
2	MAX	chr7:139477743-139478691	SK-N-SH	brain:	n/a	n/a
3	ZBTB7A	chr7:139476625-139478556	K562	blood:	n/a	chr7:139478411-139478422
4	SRF	chr7:139477766-139478226	MCF-7	breast:	n/a	n/a
5	ZMIZ1	chr7:139477867-139478327	K562	blood:	n/a	n/a
6	CTCF	chr7:139478160-139478310	GM06990	blood:	n/a	n/a
7	EGR1	chr7:139477689-139478463	K562	blood:	n/a	chr7:139477845-139477859
8	POLR2A	chr7:139477624-139478229	K562	blood:	n/a	n/a
9	CREB1	chr7:139477697-139478481	HepG2	liver:	n/a	n/a
10	POLR2A	chr7:139477858-139478276	GM12878	blood:	n/a	n/a
11	EP300	chr7:139477923-139478222	GM12878	blood:	n/a	chr7:139477996-139478012 chr7:139477956-139477965 chr7:139477992-139478008
12	POLR2A	chr7:139477673-139478476	GM12878	blood:	n/a	n/a
13	MAX	chr7:139477699-139478790	A549	lung:	n/a	n/a
14	MAX	chr7:139477773-139478489	K562	blood:	n/a	n/a
15	HMGN3	chr7:139477796-139478537	K562	blood:	n/a	n/a
16	POLR2A	chr7:139477348-139478485	GM12892	blood:	n/a	n/a
17	E2F6	chr7:139477754-139478586	K562	blood:	n/a	chr7:139477956-139477965 chr7:139478402-139478412
18	NR2C2	chr7:139477763-139478201	GM12878	blood:	n/a	n/a
19	POLR2A	chr7:139477833-139478240	A549	lung:	n/a	n/a
20	GABPA	chr7:139477728-139478465	K562	blood:	n/a	n/a
21	NR3C1	chr7:139477687-139478228	A549	lung:	n/a	chr7:139478007-139478020
22	BRCA1	chr7:139478144-139478179	HepG2	liver:	n/a	n/a
23	RAD21	chr7:139477870-139479102	IMR90	lung:	n/a	n/a
24	CREB1	chr7:139477695-139478463	K562	blood:	n/a	n/a
25	POLR2A	chr7:139477667-139478347	K562	blood:	n/a	n/a
26	MAX	chr7:139477706-139478590	H1-hESC	embryonic stem cell:	n/a	n/a
27	HA-E2F1	chr7:139477371-139478317	Hela-S3	cervix:	n/a	chr7:139477956-139477965 chr7:139477552-139477561
28	POLR2A	chr7:139477759-139478274	HepG2	liver:	n/a	n/a
29	MXI1	chr7:139477827-139478614	GM12878	blood:	n/a	n/a
30	BCLAF1	chr7:139477700-139478234	GM12878	blood:	n/a	chr7:139477995-139478008 chr7:139477956-139477969 chr7:139477950-139477963
31	MAZ	chr7:139477759-139478412	GM12878	blood:	n/a	n/a
32	POLR2A	chr7:139477403-139478384	HUVEC	blood vessel:	n/a	n/a
33	YY1	chr7:139476538-139479022	SK-N-SH	brain:	n/a	chr7:139477424-139477435 chr7:139477529-139477543 chr7:139477955-139477969 chr7:139477902-139477921 chr7:139477412-139477432 chr7:139477226-139477240 chr7:139477901-139477921 chr7:139477535-139477546 chr7:139477507-139477515 chr7:139477989-139478000
34	TCF3	chr7:139477867-139478295	GM12878	blood:	n/a	n/a
35	POLR2A	chr7:139477364-139478621	GM19193	blood:	n/a	n/a
36	MYC	chr7:139477786-139478574	K562	blood:	n/a	n/a
37	POLR2A	chr7:139477850-139478289	A549	lung:	n/a	n/a
38	POLR2A	chr7:139476514-139478674	K562	blood:	n/a	n/a
39	HEY1	chr7:139477852-139478209	K562	blood:	n/a	chr7:139477989-139478004 chr7:139477955-139477970
40	MAX	chr7:139477647-139478860	A549	lung:	n/a	n/a
41	BACH1	chr7:139477886-139478568	H1-hESC	embryonic stem cell:	n/a	n/a
42	MYC	chr7:139477700-139478412	HepG2	liver:	n/a	n/a
43	ETS1	chr7:139477763-139478362	K562	blood:	n/a	n/a
44	MAZ	chr7:139477790-139478188	Hela-S3	cervix:	n/a	n/a
45	PML	chr7:139477687-139478796	GM12878	blood:	n/a	n/a
46	SETDB1	chr7:139477873-139478324	K562	blood:	n/a	n/a
47	YY1	chr7:139477682-139478360	GM12878	blood:	n/a	chr7:139477955-139477969 chr7:139477902-139477921 chr7:139477901-139477921 chr7:139477989-139478000
48	MYC	chr7:139477765-139478577	K562	blood:	n/a	n/a
49	ZNF263	chr7:139477949-139478766	HEK293-T-REx	kidney:	n/a	chr7:139478317-139478338
50	POLR2A	chr7:139477842-139478433	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26158181..26160251-chr7:139476447..139479207,2	K562	blood:
2	chr7:139476813..139479584-chr7:139529025..139531896,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBXAS1-3	chr7:139478055-139478270	NONHSAT123654
2	lnc-TBXAS1-3	chr7:139478053-139478270	NONHSAT123653

Variant related genes	Relation type
HIPK2	TF binding region
TBXAS1	TF binding region
ENSG00000059377	Chromatin interaction
ENSG00000158373	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1011017	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1011018	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1015122	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10262775	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11769215	0.84[EUR][1000 genomes]
rs11769961	0.86[EUR][1000 genomes]
rs11770283	0.90[EUR][1000 genomes]
rs12673068	0.90[EUR][1000 genomes]
rs12703395	0.88[EUR][1000 genomes]
rs1541480	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1860508	0.89[ASN][1000 genomes]
rs2058265	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2109338	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28656273	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4132077	0.85[EUR][1000 genomes]
rs4132078	0.85[EUR][1000 genomes]
rs4725579	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4726459	0.83[EUR][1000 genomes]
rs4726525	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56152277	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58543521	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6464214	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6464220	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66985026	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6978085	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7456421	0.86[EUR][1000 genomes]
rs7459106	0.89[EUR][1000 genomes]
rs7782128	0.91[EUR][1000 genomes]
rs7790519	0.92[EUR][1000 genomes]
rs7807797	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7810028	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020234	chr7:139377822-139661964	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032711	chr7:139411404-139684043	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv464732	chr7:139424022-139654256	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv608472	chr7:139424022-139654256	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1018712	chr7:139429703-139658014	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3442657	chr7:139476008-139478856	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv3374483	chr7:139476358-139478831	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3371546	chr7:139476533-139478481	Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr7:139474800-139478400	Active TSS	Right Ventricle	heart
2	chr7:139475400-139478200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:139475400-139478200	Active TSS	Thymus	Thymus
4	chr7:139475400-139478400	Active TSS	Stomach Smooth Muscle	stomach
5	chr7:139475400-139478600	Active TSS	Fetal Brain Female	brain
6	chr7:139475400-139478600	Active TSS	Lung	lung
7	chr7:139475400-139478800	Active TSS	Aorta	Aorta
8	chr7:139475400-139478800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr7:139475600-139478200	Active TSS	Gastric	stomach
10	chr7:139475600-139478200	Active TSS	Right Atrium	heart
11	chr7:139475600-139478400	Active TSS	Brain Hippocampus Middle	brain
12	chr7:139475600-139478600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:139475600-139478600	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr7:139475600-139478600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:139475600-139478600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:139475600-139478600	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr7:139475600-139478800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:139475600-139478800	Active TSS	Left Ventricle	heart
19	chr7:139475600-139478800	Active TSS	Psoas Muscle	Psoas
20	chr7:139475600-139479000	Active TSS	NHLF	lung
21	chr7:139475800-139478200	Active TSS	Primary monocytes fromperipheralblood	blood
22	chr7:139475800-139478200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:139475800-139478200	Active TSS	Adipose Nuclei	Adipose
24	chr7:139475800-139478200	Active TSS	Liver	Liver
25	chr7:139475800-139478200	Active TSS	Placenta	Placenta
26	chr7:139475800-139478200	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr7:139475800-139478200	Active TSS	GM12878-XiMat	blood
28	chr7:139475800-139478200	Active TSS	HMEC	breast
29	chr7:139475800-139478400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr7:139475800-139478400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:139475800-139478400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:139475800-139478400	Active TSS	Brain Anterior Caudate	brain
33	chr7:139475800-139478400	Active TSS	Brain Cingulate Gyrus	brain
34	chr7:139475800-139478400	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr7:139475800-139478400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr7:139475800-139478400	Active TSS	Fetal Intestine Small	intestine
37	chr7:139475800-139478400	Active TSS	Fetal Stomach	stomach
38	chr7:139475800-139478400	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr7:139475800-139478400	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr7:139475800-139478400	Active TSS	Small Intestine	intestine
41	chr7:139475800-139478400	Active TSS	NHEK	skin
42	chr7:139475800-139478600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:139475800-139478600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:139475800-139478600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr7:139475800-139478600	Active TSS	Colon Smooth Muscle	Colon
46	chr7:139475800-139478600	Active TSS	Fetal Intestine Large	intestine
47	chr7:139475800-139478600	Active TSS	Placenta Amnion	Placenta Amnion
48	chr7:139475800-139478600	Active TSS	Rectal Smooth Muscle	rectum
49	chr7:139475800-139478600	Active TSS	A549	lung
50	chr7:139475800-139478600	Active TSS	HSMMtube	muscle

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