Variant report

Variant	rs7488680
Chromosome Location	chr12:104697102-104697103
allele	G/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	ATF3	chr12:104696811-104698807	A549	lung:	n/a	n/a
2	SP1	chr12:104696322-104698630	A549	lung:	n/a	n/a
3	FOSL2	chr12:104696444-104698901	A549	lung:	n/a	n/a
4	PML	chr12:104696951-104698125	GM12878	blood:	n/a	n/a
5	ATF2	chr12:104697088-104697497	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUND	chr12:104696965-104698155	A549	lung:	n/a	n/a
7	POLR2A	chr12:104696633-104697254	K562	blood:	n/a	n/a
8	POLR2A	chr12:104696416-104698790	HUVEC	blood vessel:	n/a	n/a
9	MAZ	chr12:104696996-104698190	IMR90	lung:	n/a	n/a
10	ETS1	chr12:104697062-104698857	A549	lung:	n/a	chr12:104697900-104697907 chr12:104697692-104697703 chr12:104697872-104697881
11	POLR2A	chr12:104696675-104698020	GM12892	blood:	n/a	n/a
12	YY1	chr12:104696725-104698405	A549	lung:	n/a	chr12:104697692-104697703 chr12:104698302-104698312 chr12:104697691-104697700
13	POLR2A	chr12:104696659-104698041	GM12892	blood:	n/a	n/a
14	SP1	chr12:104695282-104698790	A549	lung:	n/a	n/a
15	POLR2A	chr12:104697029-104697281	A549	lung:	n/a	n/a
16	MAX	chr12:104696465-104698833	A549	lung:	n/a	chr12:104698605-104698614
17	RUNX3	chr12:104697040-104698045	GM12878	blood:	n/a	n/a
18	TCF12	chr12:104695268-104701849	A549	lung:	n/a	n/a
19	POLR2A	chr12:104696486-104697391	K562	blood:	n/a	n/a
20	YY1	chr12:104697058-104697997	GM12892	blood:	n/a	chr12:104697692-104697703 chr12:104697691-104697700
21	POLR2A	chr12:104696354-104701825	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr12:104696544-104702660	HepG2	liver:	n/a	n/a
23	POLR2A	chr12:104684682-104705657	A549	lung:	n/a	n/a
24	TCF12	chr12:104696922-104698469	A549	lung:	n/a	n/a
25	SIX5	chr12:104695288-104701950	A549	lung:	n/a	chr12:104700345-104700361 chr12:104699538-104699547 chr12:104698479-104698493 chr12:104700866-104700882
26	REST	chr12:104696751-104697313	A549	lung:	n/a	n/a
27	REST	chr12:104696446-104701824	A549	lung:	n/a	chr12:104698081-104698101 chr12:104697868-104697886 chr12:104698081-104698101 chr12:104698082-104698100 chr12:104698081-104698101
28	POLR2A	chr12:104697098-104697150	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:104696471-104698728	HUVEC	blood vessel:	n/a	n/a
30	JUN	chr12:104696699-104697152	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr12:104696555-104698600	Hela-S3	cervix:	n/a	n/a
32	MAX	chr12:104696614-104698343	A549	lung:	n/a	n/a
33	STAT5A	chr12:104697100-104697777	GM12878	blood:	n/a	chr12:104697610-104697630 chr12:104697616-104697624 chr12:104697610-104697630 chr12:104697616-104697625 chr12:104697615-104697624
34	PAX5	chr12:104696942-104697255	GM12878	blood:	n/a	n/a
35	POLR2A	chr12:104696508-104697208	HCT-116	colon:	n/a	n/a
36	POLR2A	chr12:104696637-104697373	K562	blood:	n/a	n/a
37	SIN3AK20	chr12:104696527-104697457	A549	lung:	n/a	n/a
38	E2F6	chr12:104697060-104698610	A549	lung:	n/a	n/a
39	POLR2A	chr12:104697102-104698074	GM12878	blood:	n/a	n/a
40	MAX	chr12:104696603-104698042	A549	lung:	n/a	n/a
41	MTA3	chr12:104696698-104698028	GM12878	blood:	n/a	n/a
42	POLR2A	chr12:104696582-104698543	HepG2	liver:	n/a	n/a
43	ATF2	chr12:104697078-104697471	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr12:104696977-104697937	GM12892	blood:	n/a	n/a
45	BCL3	chr12:104696506-104698772	A549	lung:	n/a	chr12:104697692-104697701 chr12:104697695-104697704
46	MXI1	chr12:104696857-104698994	IMR90	lung:	n/a	n/a
47	POLR2A	chr12:104696376-104698758	Hela-S3	cervix:	n/a	n/a
48	FOSL2	chr12:104697022-104697413	A549	lung:	n/a	n/a
49	POLR2A	chr12:104697102-104697252	A549	lung:	n/a	n/a
50	WRNIP1	chr12:104697022-104697222	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104681069..104682728-chr12:104694338..104697222,2	MCF-7	breast:
2	chr12:104696590..104698591-chr12:104702374..104705113,2	MCF-7	breast:
3	chr12:104680142..104683904-chr12:104694272..104698636,5	MCF-7	breast:

Variant related genes	Relation type
EID3	TF binding region
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10778321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861185	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs10861187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861190	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861193	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861195	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861196	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861197	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861198	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861199	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861208	0.89[ASN][1000 genomes]
rs11111938	0.85[JPT][hapmap]
rs11111940	0.86[JPT][hapmap]
rs11111945	0.81[JPT][hapmap]
rs11111960	0.91[GIH][hapmap]
rs11111979	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111981	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111984	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111987	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111995	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111996	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112006	0.92[ASN][1000 genomes]
rs11609469	0.89[ASN][1000 genomes]
rs12811618	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17202060	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17202520	0.92[ASN][1000 genomes]
rs4075411	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4445711	0.86[JPT][hapmap]
rs4595619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4601859	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964782	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964783	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964785	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5018287	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132675	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294778	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297956	0.82[JPT][hapmap]
rs7298739	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310815	0.81[JPT][hapmap]
rs7954970	0.84[JPT][hapmap]
rs7958262	0.86[JPT][hapmap]
rs7977410	0.94[ASN][1000 genomes]
rs7977553	0.92[ASN][1000 genomes]
rs7978051	0.92[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	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1048075	chr12:104694799-104751460	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv541588	chr12:104694799-104751460	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv52994	chr12:104696286-104701777	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7488680	EID3	cis	normal skin	skin_eQTL
rs7488680	EID3	cis	Adipose Subcutaneous	GTEx
rs7488680	TCP11L2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104683800-104723800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:104686200-104700600	Strong transcription	Dnd41	blood
3	chr12:104686400-104697600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:104687200-104700600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:104687600-104697400	Weak transcription	Gastric	stomach
6	chr12:104689600-104697400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:104690400-104697600	Weak transcription	Lung	lung
8	chr12:104690800-104698000	Genic enhancers	Hela-S3	cervix
9	chr12:104691200-104702200	Transcr. at gene 5' and 3'	A549	lung
10	chr12:104691800-104703400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:104693400-104697200	Weak transcription	Aorta	Aorta
12	chr12:104694800-104697200	Weak transcription	HepG2	liver
13	chr12:104695600-104697200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:104695800-104700800	Strong transcription	K562	blood
15	chr12:104696200-104698400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:104696400-104697200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
17	chr12:104696600-104697200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr12:104696600-104697200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr12:104696600-104697200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr12:104696600-104697200	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr12:104696600-104697200	Flanking Active TSS	Right Ventricle	heart
22	chr12:104696600-104697200	Flanking Active TSS	GM12878-XiMat	blood
23	chr12:104696600-104697400	Enhancers	Small Intestine	intestine
24	chr12:104696600-104697800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:104696600-104698200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
26	chr12:104696600-104698400	Transcr. at gene 5' and 3'	Osteobl	bone
27	chr12:104696600-104701600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:104696800-104697200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr12:104696800-104697200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr12:104696800-104697200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:104696800-104697200	Enhancers	Primary B cells from cord blood	blood
32	chr12:104696800-104697200	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr12:104696800-104697200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:104696800-104697200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr12:104696800-104697200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:104696800-104697200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:104696800-104697200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:104696800-104697200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:104696800-104697200	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr12:104696800-104697200	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr12:104696800-104697200	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr12:104696800-104697200	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr12:104696800-104697200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr12:104696800-104697200	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr12:104696800-104697200	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr12:104696800-104697200	Flanking Active TSS	Fetal Lung	lung
47	chr12:104696800-104697200	Enhancers	Left Ventricle	heart
48	chr12:104696800-104697200	Flanking Active TSS	Psoas Muscle	Psoas
49	chr12:104696800-104697200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr12:104696800-104697200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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