Variant report

Variant	rs38414
Chromosome Location	chr7:30544360-30544361
allele	A/G
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	TCF12	chr7:30544243-30544492	GM12878	blood:	n/a	n/a
2	MAZ	chr7:30543684-30544834	Hela-S3	cervix:	n/a	chr7:30544110-30544119
3	FOXA1	chr7:30544275-30544813	T-47D	breast:	n/a	n/a
4	HCFC1	chr7:30544161-30545053	K562	blood:	n/a	n/a
5	SIN3AK20	chr7:30544106-30544500	A549	lung:	n/a	n/a
6	CBX3	chr7:30544132-30545117	K562	blood:	n/a	n/a
7	FOXP2	chr7:30544309-30544687	SK-N-MC	brain:	n/a	n/a
8	MYC	chr7:30543779-30545117	K562	blood:	n/a	chr7:30544110-30544119
9	POLR2A	chr7:30543199-30545052	HepG2	liver:	n/a	n/a
10	POLR2A	chr7:30543923-30544951	GM12878	blood:	n/a	n/a
11	MYC	chr7:30544230-30544789	HepG2	liver:	n/a	n/a
12	TAF1	chr7:30544145-30544869	K562	blood:	n/a	n/a
13	BCLAF1	chr7:30544084-30545000	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:30543991-30545051	HUVEC	blood vessel:	n/a	n/a
15	SP1	chr7:30544316-30544834	K562	blood:	n/a	chr7:30544556-30544570 chr7:30544481-30544502 chr7:30544605-30544626 chr7:30544521-30544542 chr7:30544638-30544647
16	CEBPB	chr7:30544255-30544894	MCF-7	breast:	n/a	chr7:30544492-30544500
17	UBTF	chr7:30544095-30545069	K562	blood:	n/a	n/a
18	CTCF	chr7:30544300-30544450	AG10803	skin:	n/a	n/a
19	RCOR1	chr7:30543793-30544946	GM12878	blood:	n/a	n/a
20	POLR2A	chr7:30543622-30545568	GM12891	blood:	n/a	n/a
21	MXI1	chr7:30544116-30544835	K562	blood:	n/a	n/a
22	TAF1	chr7:30543972-30545173	ECC-1	luminal epithelium:	n/a	n/a
23	MAX	chr7:30543915-30545006	K562	blood:	n/a	chr7:30544110-30544119
24	MYC	chr7:30543939-30544906	K562	blood:	n/a	chr7:30544110-30544119
25	POLR2A	chr7:30543764-30545088	GM12892	blood:	n/a	n/a
26	POLR2A	chr7:30544188-30544924	HepG2	liver:	n/a	n/a
27	REST	chr7:30543602-30544981	A549	lung:	n/a	chr7:30544016-30544029
28	POLR2A	chr7:30544240-30544528	A549	lung:	n/a	n/a
29	POLR2A	chr7:30543852-30544941	H1-hESC	embryonic stem cell:	n/a	n/a
30	SP1	chr7:30544142-30544896	GM12878	blood:	n/a	chr7:30544556-30544570 chr7:30544481-30544502 chr7:30544605-30544626 chr7:30544521-30544542 chr7:30544638-30544647
31	RFX5	chr7:30544290-30545080	HepG2	liver:	n/a	chr7:30544491-30544500
32	POLR2A	chr7:30544046-30545091	GM12878	blood:	n/a	n/a
33	GABPA	chr7:30543876-30545163	MCF-7	breast:	n/a	n/a
34	MYC	chr7:30543630-30545220	NB4	blood:	n/a	chr7:30544110-30544119 chr7:30545195-30545205
35	YY1	chr7:30544235-30544947	HCT-116	colon:	n/a	n/a
36	JUND	chr7:30544305-30544467	H1-hESC	embryonic stem cell:	n/a	n/a
37	TCF12	chr7:30543964-30544977	ECC-1	luminal epithelium:	n/a	chr7:30544094-30544102
38	FOXM1	chr7:30543789-30544858	GM12878	blood:	n/a	n/a
39	BHLHE40	chr7:30544211-30544882	HepG2	liver:	n/a	n/a
40	POLR2A	chr7:30544165-30544961	K562	blood:	n/a	n/a
41	POLR2A	chr7:30544000-30545224	HUVEC	blood vessel:	n/a	n/a
42	PML	chr7:30544001-30545135	GM12878	blood:	n/a	n/a
43	SMARCB1	chr7:30543759-30545057	Hela-S3	cervix:	n/a	n/a
44	CEBPB	chr7:30543775-30544847	HepG2	liver:	n/a	chr7:30544492-30544500
45	ZNF143	chr7:30544314-30544825	K562	blood:	n/a	n/a
46	SP1	chr7:30544197-30544883	HepG2	liver:	n/a	chr7:30544556-30544570 chr7:30544481-30544502 chr7:30544605-30544626 chr7:30544521-30544542 chr7:30544638-30544647
47	TAF1	chr7:30543811-30544995	H1-hESC	embryonic stem cell:	n/a	n/a
48	ELF1	chr7:30543818-30544912	MCF-7	breast:	n/a	n/a
49	RFX5	chr7:30544161-30544805	GM12878	blood:	n/a	chr7:30544491-30544500
50	NFYB	chr7:30544088-30544981	K562	blood:	n/a	chr7:30544488-30544503 chr7:30544491-30544501 chr7:30544489-30544503 chr7:30544614-30544629 chr7:30544490-30544503 chr7:30544488-30544503 chr7:30544529-30544543

No.	Distal block	Cell Line	Cell type
1	chr7:30516309..30520214-chr7:30539829..30545899,10	MCF-7	breast:
2	chr7:30514482..30520047-chr7:30541597..30545999,6	K562	blood:
3	chr7:30543086..30546896-chr7:30587990..30592067,4	MCF-7	breast:
4	chr7:30542906..30546609-chr7:30564616..30567471,3	K562	blood:
5	chr7:30540102..30542723-chr7:30542755..30545795,4	K562	blood:
6	chr7:30470137..30472560-chr7:30542746..30544397,2	MCF-7	breast:
7	chr6:25992336..25992907-chr7:30543969..30544620,2	NB4	blood:
8	chr7:30322508..30325162-chr7:30542047..30544631,2	K562	blood:
9	chr22:37415018..37415812-chr7:30544114..30544657,2	NB4	blood:
10	chr7:30537997..30542227-chr7:30542503..30545909,8	MCF-7	breast:
11	chr7:30516697..30519938-chr7:30542758..30546445,6	K562	blood:
12	chr7:30516038..30518897-chr7:30540788..30545615,6	MCF-7	breast:
13	chr1:46151520..46152279-chr7:30544339..30545254,2	Hela-S3	cervix:

Variant related genes	Relation type
GGCT	TF binding region
ENSG00000264520	Chromatin interaction
ENSG00000272462	Chromatin interaction
ENSG00000196295	Chromatin interaction
ENSG00000006625	Chromatin interaction
ENSG00000128309	Chromatin interaction
ENSG00000180233	Chromatin interaction
ENSG00000263683	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000106100	Chromatin interaction
ENSG00000128311	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs28679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38406	0.87[ASN][1000 genomes]
rs38407	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38408	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38409	0.86[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs38410	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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38413	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38415	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs38416	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38417	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38418	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38419	0.99[ASN][1000 genomes]
rs38420	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38421	0.94[ASN][1000 genomes]
rs38422	0.99[ASN][1000 genomes]
rs38423	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38425	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38426	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38427	0.99[ASN][1000 genomes]
rs38428	0.88[ASN][1000 genomes]
rs38429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38430	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38432	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38433	0.91[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38434	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38435	0.87[ASN][1000 genomes]
rs38436	0.87[ASN][1000 genomes]
rs38437	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38438	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38440	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38441	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38442	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38443	0.84[ASN][1000 genomes]
rs38444	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38445	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38446	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38447	0.81[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs38448	0.89[ASN][1000 genomes]
rs38450	0.81[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs38451	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38452	0.89[ASN][1000 genomes]
rs38453	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38454	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38455	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38456	0.88[ASN][1000 genomes]
rs38458	0.88[ASN][1000 genomes]
rs38460	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38461	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38462	0.88[ASN][1000 genomes]
rs38463	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38464	0.88[ASN][1000 genomes]
rs38465	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38466	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs38467	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38468	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38469	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38471	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38472	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38473	0.80[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs38474	0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38478	0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs38480	0.84[CEU][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38481	0.82[ASN][1000 genomes]
rs38482	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs38483	0.81[ASN][1000 genomes]
rs38487	0.81[GIH][hapmap]
rs39738	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs40237	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4259	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4260	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs38414	CRHR2	cis	parietal	SCAN
rs38414	AC005154.6	cis	Stomach	GTEx
rs38414	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38414	AC005154.6	cis	Artery Tibial	GTEx
rs38414	AC005154.8	cis	Whole Blood	GTEx
rs38414	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38414	AC005154.6	cis	Whole Blood	GTEx
rs38414	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38414	AC005154.6	cis	lung	GTEx
rs38414	AC005154.6	cis	Muscle Skeletal	GTEx
rs38414	AC005154.6	cis	Esophagus Mucosa	GTEx
rs38414	AC005154.6	cis	Artery Aorta	GTEx
rs38414	AC005154.6	cis	Nerve Tibial	GTEx
rs38414	AC005154.6	cis	Thyroid	GTEx
rs38414	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38414	AC005154.6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30542400-30545600	Active TSS	NHLF	lung
2	chr7:30542800-30544400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:30542800-30545200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:30543000-30544800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:30543000-30545200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr7:30543200-30544800	Active TSS	Fetal Intestine Small	intestine
7	chr7:30543200-30545000	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr7:30543200-30545200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr7:30543200-30545200	Active TSS	HSMMtube	muscle
10	chr7:30543200-30545400	Active TSS	A549	lung
11	chr7:30543400-30544400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:30543400-30544400	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr7:30543400-30544800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:30543400-30544800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:30543400-30544800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:30543400-30544800	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr7:30543400-30544800	Active TSS	GM12878-XiMat	blood
18	chr7:30543400-30545000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr7:30543400-30545000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:30543400-30545200	Active TSS	H1 Cell Line	embryonic stem cell
21	chr7:30543400-30545200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:30543400-30545200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:30543400-30545200	Active TSS	Esophagus	oesophagus
24	chr7:30543400-30545200	Active TSS	Fetal Brain Female	brain
25	chr7:30543400-30545200	Active TSS	Left Ventricle	heart
26	chr7:30543400-30545200	Active TSS	Lung	lung
27	chr7:30543400-30545200	Active TSS	Ovary	ovary
28	chr7:30543400-30545200	Active TSS	Psoas Muscle	Psoas
29	chr7:30543400-30545200	Active TSS	Right Atrium	heart
30	chr7:30543400-30545200	Active TSS	NHDF-Ad	bronchial
31	chr7:30543400-30545600	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr7:30543600-30544400	Bivalent/Poised TSS	HepG2	liver
33	chr7:30543600-30544600	Active TSS	Hela-S3	cervix
34	chr7:30543600-30544800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:30543600-30544800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:30543600-30544800	Active TSS	Fetal Muscle Trunk	muscle
37	chr7:30543600-30545000	Active TSS	Pancreas	Pancrea
38	chr7:30543600-30545000	Active TSS	Placenta Amnion	Placenta Amnion
39	chr7:30543600-30545000	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr7:30543600-30545000	Active TSS	Stomach Mucosa	stomach
41	chr7:30543600-30545200	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr7:30543600-30545200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr7:30543600-30545200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr7:30543600-30545200	Active TSS	Muscle Satellite Cultured Cells	--
45	chr7:30543600-30545200	Active TSS	Fetal Intestine Large	intestine
46	chr7:30543600-30545200	Active TSS	Fetal Kidney	kidney
47	chr7:30543600-30545200	Active TSS	Gastric	stomach
48	chr7:30543600-30545400	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr7:30543600-30545400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr7:30543800-30544400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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