Variant report

Variant	rs2525740
Chromosome Location	chr7:120629481-120629482
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	SMC3	chr7:120626321-120630414	SK-N-SH	brain:	n/a	chr7:120628784-120628794 chr7:120627827-120627841
2	POLR2A	chr7:120627756-120630200	K562	blood:	n/a	n/a
3	IRF1	chr7:120627116-120635409	K562	blood:	n/a	chr7:120630359-120630372 chr7:120627249-120627263 chr7:120631335-120631349 chr7:120631339-120631352 chr7:120631339-120631352 chr7:120635391-120635408 chr7:120630358-120630365 chr7:120631333-120631353 chr7:120628715-120628729 chr7:120635200-120635214 chr7:120631338-120631352 chr7:120630359-120630370 chr7:120631712-120631728 chr7:120634512-120634525 chr7:120632017-120632026 chr7:120631336-120631347 chr7:120630266-120630273 chr7:120631339-120631359 chr7:120631762-120631769 chr7:120634516-120634533
4	SPI1	chr7:120628840-120629516	HL-60	blood:	n/a	chr7:120629166-120629179
5	ARID3A	chr7:120627387-120629832	K562	blood:	n/a	n/a
6	SIN3AK20	chr7:120628416-120629816	SK-N-SH	brain:	n/a	n/a
7	RAD21	chr7:120626694-120630432	SK-N-SH	brain:	n/a	chr7:120628734-120628747 chr7:120628739-120628752 chr7:120628735-120628749
8	POLR2A	chr7:120627807-120630114	K562	blood:	n/a	n/a
9	POLR2A	chr7:120629472-120629944	K562	blood:	n/a	n/a
10	MXI1	chr7:120627591-120630197	IMR90	lung:	n/a	n/a
11	TEAD4	chr7:120627191-120630447	K562	blood:	n/a	n/a
12	TBL1XR1	chr7:120627300-120634804	K562	blood:	n/a	n/a
13	MAFK	chr7:120627507-120629508	K562	blood:	n/a	n/a
14	TCF12	chr7:120627585-120630275	SK-N-SH	brain:	n/a	chr7:120628683-120628693
15	STAT5A	chr7:120627202-120630414	K562	blood:	n/a	chr7:120628729-120628741 chr7:120628941-120628949
16	POLR2A	chr7:120627674-120630288	IMR90	lung:	n/a	n/a
17	PML	chr7:120627185-120629563	K562	blood:	n/a	chr7:120628701-120628709
18	RCOR1	chr7:120626702-120629554	K562	blood:	n/a	n/a
19	IRF1	chr7:120627326-120635792	K562	blood:	n/a	chr7:120630359-120630372 chr7:120631335-120631349 chr7:120631339-120631352 chr7:120631339-120631352 chr7:120635391-120635408 chr7:120630358-120630365 chr7:120631333-120631353 chr7:120628715-120628729 chr7:120635200-120635214 chr7:120631338-120631352 chr7:120630359-120630370 chr7:120631712-120631728 chr7:120634512-120634525 chr7:120632017-120632026 chr7:120631336-120631347 chr7:120630266-120630273 chr7:120631339-120631359 chr7:120631762-120631769 chr7:120634516-120634533
20	POLR2A	chr7:120627741-120630346	K562	blood:	n/a	n/a
21	CTCF	chr7:120627322-120630069	SK-N-SH	brain:	n/a	chr7:120627825-120627843 chr7:120627828-120627841 chr7:120628735-120628748 chr7:120628739-120628748 chr7:120627826-120627842
22	NFIC	chr7:120628426-120630221	SK-N-SH	brain:	n/a	n/a
23	UBTF	chr7:120627678-120630365	K562	blood:	n/a	n/a
24	TBP	chr7:120627483-120630188	K562	blood:	n/a	n/a
25	MXI1	chr7:120626776-120632296	SK-N-SH	brain:	n/a	n/a
26	TAF7	chr7:120628944-120629698	K562	blood:	n/a	n/a
27	UBTF	chr7:120627639-120630236	K562	blood:	n/a	n/a
28	CREB1	chr7:120627197-120631738	K562	blood:	n/a	n/a
29	MYC	chr7:120627096-120630340	K562	blood:	n/a	chr7:120628078-120628088 chr7:120628900-120628909
30	PAX5	chr7:120629419-120629927	GM12878	blood:	n/a	n/a
31	POLR2A	chr7:120627780-120630249	K562	blood:	n/a	n/a
32	MYC	chr7:120627394-120629554	K562	blood:	n/a	chr7:120628078-120628088 chr7:120628900-120628909
33	MAX	chr7:120628537-120630263	SK-N-SH	brain:	n/a	chr7:120628900-120628909
34	PAX5	chr7:120629479-120629877	GM12878	blood:	n/a	n/a
35	POLR2A	chr7:120629301-120629750	K562	blood:	n/a	n/a
36	POLR2A	chr7:120627391-120630036	K562	blood:	n/a	n/a
37	CCNT2	chr7:120628507-120630106	K562	blood:	n/a	n/a
38	JUN	chr7:120627664-120629592	K562	blood:	n/a	chr7:120628045-120628054

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120621518..120649031-chr7:120712706..120728931,108	K562	blood:
2	chr7:120624020..120645873-chr7:120713358..120727138,77	K562	blood:

Variant related genes	Relation type
CPED1	TF binding region
ENSG00000106034	Chromatin interaction
ENSG00000212628	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10229719	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10258025	0.96[EUR][1000 genomes]
rs11363	0.81[EUR][1000 genomes]
rs12672149	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13881	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs193727	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2013083	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2013087	0.84[CEU][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs2074576	0.90[CEU][hapmap]
rs2074577	0.85[CEU][hapmap]
rs2215786	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2215789	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2244863	0.85[CEU][hapmap]
rs2244865	0.85[CEU][hapmap]
rs2525711	1.00[CEU][hapmap]
rs2525712	0.85[CEU][hapmap]
rs2525713	0.85[CEU][hapmap]
rs2525714	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs2525715	1.00[CEU][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2525716	1.00[CEU][hapmap]
rs2525717	1.00[CEU][hapmap]
rs2525718	0.90[CEU][hapmap]
rs2525719	0.90[CEU][hapmap]
rs2525720	1.00[CEU][hapmap]
rs2525722	0.94[CEU][hapmap]
rs2525724	1.00[CEU][hapmap]
rs2525725	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2525726	1.00[CEU][hapmap]
rs2525728	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2525731	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2525732	0.82[EUR][1000 genomes]
rs2525733	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2525734	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2525735	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2525736	0.82[EUR][1000 genomes]
rs2525738	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525741	0.85[EUR][1000 genomes]
rs2538485	0.84[MEX][hapmap]
rs2721350	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2721351	0.89[CEU][hapmap]
rs2721358	0.85[EUR][1000 genomes]
rs2721359	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721361	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721363	0.80[EUR][1000 genomes]
rs2721366	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2721368	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs2721370	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2721372	0.90[CEU][hapmap]
rs2896299	0.84[CEU][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3944026	1.00[CEU][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41688	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs41689	0.85[EUR][1000 genomes]
rs41691	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41693	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41694	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41695	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41697	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41703	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs41704	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs4727915	0.84[CEU][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4730985	0.83[CEU][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4730987	0.82[AMR][1000 genomes]
rs6966297	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6973457	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7789501	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7808535	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2525740	SPAM1	cis	parietal	SCAN
rs2525740	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120627600-120633800	Active TSS	Stomach Smooth Muscle	stomach
2	chr7:120627800-120629600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:120627800-120629800	Active TSS	Brain Angular Gyrus	brain
4	chr7:120627800-120629800	Active TSS	Fetal Lung	lung
5	chr7:120627800-120629800	Active TSS	Pancreas	Pancrea
6	chr7:120627800-120630200	Active TSS	Brain Substantia Nigra	brain
7	chr7:120627800-120630400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:120627800-120631200	Active TSS	Left Ventricle	heart
9	chr7:120627800-120632000	Active TSS	Brain Hippocampus Middle	brain
10	chr7:120627800-120632000	Active TSS	Psoas Muscle	Psoas
11	chr7:120627800-120632200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:120627800-120632200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:120627800-120632400	Active TSS	Colon Smooth Muscle	Colon
14	chr7:120627800-120633000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:120627800-120633000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:120627800-120633000	Active TSS	NHDF-Ad	bronchial
17	chr7:120627800-120633200	Active TSS	Right Atrium	heart
18	chr7:120627800-120633600	Active TSS	Ovary	ovary
19	chr7:120627800-120633800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:120627800-120633800	Active TSS	Aorta	Aorta
21	chr7:120627800-120633800	Active TSS	Right Ventricle	heart
22	chr7:120628000-120629600	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr7:120628000-120629600	Active TSS	Fetal Muscle Trunk	muscle
24	chr7:120628000-120629800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr7:120628000-120630000	Active TSS	Lung	lung
26	chr7:120628200-120629600	Active TSS	Fetal Stomach	stomach
27	chr7:120628200-120630000	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr7:120628200-120630200	Active TSS	Placenta	Placenta
29	chr7:120628200-120631200	Active TSS	Brain Anterior Caudate	brain
30	chr7:120628200-120632400	Active TSS	Rectal Smooth Muscle	rectum
31	chr7:120628200-120632400	Active TSS	K562	blood
32	chr7:120628200-120633800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:120628400-120629600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr7:120628400-120632400	Active TSS	HSMM	muscle
35	chr7:120628400-120633000	Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr7:120628600-120629600	Active TSS	Adipose Nuclei	Adipose
37	chr7:120628600-120629600	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr7:120628600-120629600	Active TSS	Hela-S3	cervix
39	chr7:120628600-120629600	Active TSS	Osteobl	bone
40	chr7:120628600-120630200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:120628600-120631600	Active TSS	Liver	Liver
42	chr7:120628600-120632600	Active TSS	Fetal Muscle Leg	muscle
43	chr7:120628600-120633000	Active TSS	HSMMtube	muscle
44	chr7:120628800-120633600	Active TSS	NHLF	lung
45	chr7:120629000-120629600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:120629000-120629600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr7:120629000-120629600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
48	chr7:120629000-120629600	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr7:120629000-120629800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr7:120629000-120629800	Active TSS	Colonic Mucosa	Colon

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