Variant report

Variant	rs3814460
Chromosome Location	chr7:120497450-120497451
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	POLR2A	chr7:120496702-120498414	GM12892	blood:	n/a	n/a
2	SMC3	chr7:120496700-120498041	GM12878	blood:	n/a	chr7:120496890-120496900
3	CREB1	chr7:120496782-120497506	H1-hESC	embryonic stem cell:	n/a	chr7:120497289-120497302
4	HA-E2F1	chr7:120497163-120498025	Hela-S3	cervix:	n/a	chr7:120497755-120497765 chr7:120497812-120497822 chr7:120497724-120497733 chr7:120497620-120497629
5	RCOR1	chr7:120496763-120498408	K562	blood:	n/a	n/a
6	POLR2A	chr7:120497446-120498453	GM12892	blood:	n/a	n/a
7	RAD21	chr7:120497429-120498382	H1-hESC	embryonic stem cell:	n/a	chr7:120497805-120497817 chr7:120498201-120498215
8	ZNF143	chr7:120496669-120498419	GM12878	blood:	n/a	n/a
9	CTCF	chr7:120496645-120498422	A549	lung:	n/a	chr7:120496887-120496900 chr7:120497812-120497825 chr7:120497726-120497739 chr7:120497091-120497099 chr7:120496884-120496902 chr7:120496964-120496977
10	POU2F2	chr7:120496563-120497456	GM12878	blood:	n/a	chr7:120496650-120496665 chr7:120496890-120496902
11	RAD21	chr7:120496618-120497908	GM12878	blood:	n/a	chr7:120497805-120497817 chr7:120496890-120496900 chr7:120496888-120496901 chr7:120497274-120497286
12	MAX	chr7:120496843-120497451	A549	lung:	n/a	n/a
13	HMGN3	chr7:120496840-120498561	K562	blood:	n/a	n/a
14	E2F6	chr7:120496759-120497458	H1-hESC	embryonic stem cell:	n/a	chr7:120496893-120496902 chr7:120496893-120496905
15	CTCF	chr7:120496690-120498455	GM12878	blood:	n/a	chr7:120496887-120496900 chr7:120497812-120497825 chr7:120497726-120497739 chr7:120497091-120497099 chr7:120496884-120496902 chr7:120496964-120496977
16	POLR2A	chr7:120496077-120498566	GM12878	blood:	n/a	n/a
17	POLR2A	chr7:120497109-120498678	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr7:120496147-120498481	GM12878	blood:	n/a	n/a
19	EBF1	chr7:120496086-120498448	GM12878	blood:	n/a	chr7:120497153-120497163 chr7:120496862-120496873
20	MAZ	chr7:120496803-120498378	K562	blood:	n/a	chr7:120498017-120498027 chr7:120497893-120497902
21	POLR2A	chr7:120496607-120498381	GM19193	blood:	n/a	n/a
22	MAX	chr7:120496637-120497459	H1-hESC	embryonic stem cell:	n/a	n/a
23	ZBTB7A	chr7:120497042-120498010	ECC-1	luminal epithelium:	n/a	chr7:120497654-120497663
24	MAX	chr7:120496977-120497457	MCF-7	breast:	n/a	n/a
25	POLR2A	chr7:120496700-120498385	GM15510	blood:	n/a	n/a
26	POLR2A	chr7:120496541-120498473	GM12878	blood:	n/a	n/a
27	POLR2A	chr7:120496079-120498638	GM12878	blood:	n/a	n/a
28	ZBTB7A	chr7:120496905-120498571	ECC-1	luminal epithelium:	n/a	chr7:120497654-120497663
29	CTCF	chr7:120497300-120497450	HRPEpiC	eye:	n/a	n/a
30	MAX	chr7:120496802-120498341	K562	blood:	n/a	chr7:120498017-120498027 chr7:120497893-120497902
31	ZBTB7A	chr7:120497438-120498298	K562	blood:	n/a	chr7:120497654-120497663
32	MAX	chr7:120497166-120498673	Hela-S3	cervix:	n/a	chr7:120498017-120498027 chr7:120497893-120497902
33	UBTF	chr7:120496862-120498417	K562	blood:	n/a	n/a
34	E2F6	chr7:120496775-120498389	K562	blood:	n/a	chr7:120498020-120498030 chr7:120498160-120498170 chr7:120497755-120497765 chr7:120497812-120497822 chr7:120497724-120497733 chr7:120497620-120497629 chr7:120496893-120496902 chr7:120496893-120496905 chr7:120498019-120498028
35	CTCF	chr7:120497070-120498321	K562	blood:	n/a	chr7:120497812-120497825 chr7:120497726-120497739 chr7:120497091-120497099
36	SMC3	chr7:120497174-120498603	Hela-S3	cervix:	n/a	chr7:120498036-120498046
37	MAX	chr7:120496670-120497477	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr7:120496770-120498657	HCT-116	colon:	n/a	chr7:120498017-120498027 chr7:120497893-120497902
39	MAZ	chr7:120496211-120498377	GM12878	blood:	n/a	chr7:120498017-120498027 chr7:120497893-120497902
40	BHLHE40	chr7:120496265-120498341	GM12878	blood:	n/a	chr7:120497810-120497826 chr7:120497813-120497829 chr7:120498024-120498040 chr7:120498161-120498177 chr7:120498169-120498185
41	REST	chr7:120497449-120498522	H1-neurons	neurons:	n/a	chr7:120498170-120498183 chr7:120497826-120497839 chr7:120497881-120497894 chr7:120498106-120498119 chr7:120498118-120498127 chr7:120497881-120497894
42	MAX	chr7:120496909-120497451	A549	lung:	n/a	n/a
43	CTCF	chr7:120497300-120497450	A549	lung:	n/a	n/a
44	MAX	chr7:120496726-120498547	HCT-116	colon:	n/a	chr7:120498017-120498027 chr7:120497893-120497902
45	POLR2A	chr7:120496365-120498407	GM18951	blood:	n/a	n/a
46	MAX	chr7:120496298-120498370	GM12878	blood:	n/a	chr7:120498017-120498027 chr7:120497893-120497902
47	POLR2A	chr7:120497356-120498615	H1-hESC	embryonic stem cell:	n/a	n/a
48	SIN3A	chr7:120496731-120498381	H1-hESC	embryonic stem cell:	n/a	chr7:120498170-120498183 chr7:120497878-120497891 chr7:120497732-120497743
49	POLR2A	chr7:120496631-120498406	GM19099	blood:	n/a	n/a
50	SMARCB1	chr7:120496861-120498378	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:3072484..3075327-chr7:120496877..120499119,2	MCF-7	breast:
2	chr7:120495769..120499665-chr7:120588624..120592417,7	MCF-7	breast:

Variant related genes	Relation type
TSPAN12	TF binding region
ENSG00000071243	Chromatin interaction
ENSG00000103145	Chromatin interaction
ENSG00000131652	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10225453	0.84[ASN][1000 genomes]
rs10274689	0.89[ASN][1000 genomes]
rs10279837	0.89[ASN][1000 genomes]
rs11982493	0.89[ASN][1000 genomes]
rs12669167	0.84[ASN][1000 genomes]
rs17142995	0.89[ASN][1000 genomes]
rs2040762	0.83[ASN][1000 genomes]
rs2107276	0.82[ASN][1000 genomes]
rs2524949	0.81[ASN][1000 genomes]
rs2524951	0.82[ASN][1000 genomes]
rs2721343	0.86[ASN][1000 genomes]
rs2721347	0.89[ASN][1000 genomes]
rs2721364	0.83[ASN][1000 genomes]
rs3779386	0.82[ASN][1000 genomes]
rs3823859	0.89[ASN][1000 genomes]
rs55855220	0.84[ASN][1000 genomes]
rs61452531	0.83[ASN][1000 genomes]
rs6466759	0.84[ASN][1000 genomes]
rs6466760	0.84[ASN][1000 genomes]
rs6466761	0.85[ASN][1000 genomes]
rs6466762	0.89[ASN][1000 genomes]
rs6953454	0.84[ASN][1000 genomes]
rs6958947	0.90[ASN][1000 genomes]
rs6959328	0.84[ASN][1000 genomes]
rs6964667	0.82[ASN][1000 genomes]
rs6964786	0.84[ASN][1000 genomes]
rs6971854	0.82[ASN][1000 genomes]
rs714259	0.83[ASN][1000 genomes]
rs73427805	0.82[ASN][1000 genomes]
rs73427866	0.89[ASN][1000 genomes]
rs7781985	0.90[ASN][1000 genomes]
rs7800318	0.82[ASN][1000 genomes]
rs7805211	0.85[ASN][1000 genomes]
rs996903	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv5929	chr7:120467591-120513472	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv3438279	chr7:120496341-120498889	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3814460	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120494400-120498200	Active TSS	GM12878-XiMat	blood
2	chr7:120495800-120498600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr7:120495800-120498600	Active TSS	Left Ventricle	heart
4	chr7:120496000-120499000	Active TSS	Fetal Kidney	kidney
5	chr7:120496200-120498800	Active TSS	Aorta	Aorta
6	chr7:120496200-120498800	Active TSS	Colon Smooth Muscle	Colon
7	chr7:120496200-120499000	Active TSS	Right Ventricle	heart
8	chr7:120496400-120498600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:120496400-120498600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:120496400-120498800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:120496400-120498800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr7:120496400-120498800	Active TSS	Stomach Smooth Muscle	stomach
13	chr7:120496600-120498400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:120496600-120498400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:120496600-120498400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:120496600-120498400	Active TSS	Lung	lung
17	chr7:120496600-120498600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:120496600-120498600	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr7:120496600-120498600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr7:120496600-120498600	Active TSS	Pancreas	Pancrea
21	chr7:120496600-120498600	Active TSS	Hela-S3	cervix
22	chr7:120496600-120498600	Active TSS	HSMM	muscle
23	chr7:120496600-120498800	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr7:120496600-120498800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr7:120496600-120498800	Active TSS	Brain Anterior Caudate	brain
26	chr7:120496600-120498800	Active TSS	Fetal Heart	heart
27	chr7:120496600-120498800	Active TSS	HSMMtube	muscle
28	chr7:120496600-120499000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr7:120496800-120498200	Active TSS	Colonic Mucosa	Colon
30	chr7:120496800-120498400	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr7:120496800-120498400	Transcr. at gene 5' and 3'	Right Atrium	heart
32	chr7:120496800-120498600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr7:120496800-120498600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:120496800-120498600	Active TSS	Brain Angular Gyrus	brain
35	chr7:120496800-120498600	Active TSS	Esophagus	oesophagus
36	chr7:120496800-120498600	Active TSS	Psoas Muscle	Psoas
37	chr7:120496800-120498600	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr7:120496800-120498600	Bivalent/Poised TSS	Thymus	Thymus
39	chr7:120496800-120498600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
40	chr7:120496800-120498800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:120496800-120498800	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr7:120497000-120497600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
43	chr7:120497000-120497600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
44	chr7:120497000-120498000	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
45	chr7:120497000-120498000	Active TSS	Fetal Brain Female	brain
46	chr7:120497000-120498200	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:120497000-120498400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:120497000-120498400	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr7:120497000-120498400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr7:120497000-120498400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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