Variant report

Variant	rs2074624
Chromosome Location	chr7:102985211-102985212
allele	C/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	POLR2A	chr7:102984600-102985429	GM12892	blood:	n/a	n/a
2	POLR2A	chr7:102984929-102985402	GM12878	blood:	n/a	n/a
3	NR2F2	chr7:102984910-102985454	K562	blood:	n/a	n/a
4	E2F6	chr7:102984935-102985500	A549	lung:	n/a	n/a
5	MYC	chr7:102984143-102985495	K562	blood:	n/a	chr7:102984756-102984765 chr7:102984646-102984655 chr7:102984307-102984316 chr7:102984955-102984965 chr7:102984647-102984654 chr7:102984307-102984314
6	CREB1	chr7:102984695-102985594	HepG2	liver:	n/a	n/a
7	TAF1	chr7:102984466-102985478	H1-hESC	embryonic stem cell:	n/a	n/a
8	UBTF	chr7:102984527-102985495	K562	blood:	n/a	n/a
9	SETDB1	chr7:102985042-102985510	U2OS	brain:	n/a	n/a
10	MAX	chr7:102984225-102985465	HepG2	liver:	n/a	chr7:102984756-102984765 chr7:102984646-102984655 chr7:102984307-102984316 chr7:102984955-102984965 chr7:102984647-102984654 chr7:102984307-102984314
11	ATF3	chr7:102985030-102985333	K562	blood:	n/a	n/a
12	ATF3	chr7:102984943-102985554	A549	lung:	n/a	n/a
13	POLR2A	chr7:102984568-102985523	PANC-1	pancreas:	n/a	n/a
14	MYC	chr7:102985056-102985362	GM12878	blood:	n/a	n/a
15	MYC	chr7:102985070-102985420	Hela-S3	cervix:	n/a	n/a
16	RELA	chr7:102985028-102985500	GM19099	blood:	n/a	n/a
17	GABPA	chr7:102984963-102985649	HL-60	blood:	n/a	n/a
18	POLR2A	chr7:102984511-102985513	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr7:102984362-102985479	GM12878	blood:	n/a	n/a
20	TBP	chr7:102984359-102985706	GM12878	blood:	n/a	n/a
21	CTCF	chr7:102985198-102985365	GM12878	blood:	n/a	n/a
22	MAFK	chr7:102985101-102985480	HepG2	liver:	n/a	n/a
23	CEBPB	chr7:102985164-102985295	HepG2	liver:	n/a	n/a
24	EP300	chr7:102985207-102985537	K562	blood:	n/a	chr7:102985219-102985226
25	FOXA2	chr7:102985047-102985433	A549	lung:	n/a	n/a
26	TAF1	chr7:102985025-102985518	SK-N-SH	brain:	n/a	n/a
27	GABPA	chr7:102984593-102985592	K562	blood:	n/a	n/a
28	ELF1	chr7:102984403-102985538	MCF-7	breast:	n/a	chr7:102985218-102985229 chr7:102985219-102985228 chr7:102985218-102985229
29	MAFF	chr7:102985050-102985487	HepG2	liver:	n/a	n/a
30	JUND	chr7:102984995-102985388	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr7:102984940-102985328	A549	lung:	n/a	n/a
32	MYC	chr7:102985038-102985502	K562	blood:	n/a	n/a
33	TBP	chr7:102985019-102985548	HepG2	liver:	n/a	n/a
34	PAX5	chr7:102984866-102985485	GM12878	blood:	n/a	n/a
35	MAX	chr7:102984059-102985547	MCF-7	breast:	n/a	chr7:102984756-102984765 chr7:102984646-102984655 chr7:102984307-102984316 chr7:102984955-102984965 chr7:102984647-102984654 chr7:102984307-102984314
36	MYC	chr7:102985058-102985353	MCF-7	breast:	n/a	n/a
37	BCLAF1	chr7:102985023-102985535	K562	blood:	n/a	chr7:102985218-102985227
38	YY1	chr7:102984800-102985403	HepG2	liver:	n/a	n/a
39	SRF	chr7:102985176-102985398	HepG2	liver:	n/a	n/a
40	JUND	chr7:102984276-102985516	K562	blood:	n/a	chr7:102984755-102984767 chr7:102984757-102984765 chr7:102984852-102984866
41	TEAD4	chr7:102984738-102985548	K562	blood:	n/a	n/a
42	TAF1	chr7:102985065-102985442	Hela-S3	cervix:	n/a	n/a
43	E2F6	chr7:102984175-102985474	K562	blood:	n/a	n/a
44	STAT3	chr7:102985128-102985504	MCF10A-Er-Src	breast:	n/a	n/a
45	TBL1XR1	chr7:102984731-102985509	K562	blood:	n/a	n/a
46	EGR1	chr7:102984623-102985738	HCT-116	colon:	n/a	chr7:102985265-102985280 chr7:102985263-102985277 chr7:102985266-102985279 chr7:102985218-102985227 chr7:102985091-102985101 chr7:102985267-102985276
47	POLR2A	chr7:102984270-102985479	K562	blood:	n/a	n/a
48	GABPA	chr7:102984998-102985461	GM12878	blood:	n/a	n/a
49	MYC	chr7:102983954-102985521	NB4	blood:	n/a	chr7:102984756-102984765 chr7:102984646-102984655 chr7:102984307-102984316 chr7:102984955-102984965 chr7:102984647-102984654 chr7:102984307-102984314
50	CHD1	chr7:102985069-102985505	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:102985197-102985247	RPTEC	kidney:	n/a
2	chr7:102985197-102985247	H1-hESC	embryonic stem cell:	embryo
3	chr7:102985197-102985247	SAEC	small airway:	n/a
4	chr7:102985197-102985247	K562	blood:	n/a
5	chr7:102985197-102985247	MCF-7	breast:	n/a
6	chr7:102985197-102985247	HRCEpiC	kidney:	n/a
7	chr7:102985197-102985247	ECC-1	luminal epithelium:	n/a
8	chr7:102985197-102985247	AG10803	skin:	n/a
9	chr7:102985197-102985247	PFSK-1	brain:	n/a
10	chr7:102985197-102985247	AG09319	gingival:	n/a
11	chr7:102985197-102985247	HPAEpiC	pulmonary alveolar:	n/a
12	chr7:102985197-102985247	Hepatocyte	liver:	n/a
13	chr7:102985197-102985247	NHDF-neo	bronchial:	n/a
14	chr7:102985197-102985247	HCM	heart:	n/a
15	chr7:102985197-102985247	HEK293	kidney:	embryo
16	chr7:102985197-102985247	NT2-D1	testis:	n/a
17	chr7:102985197-102985247	HL-60	blood:	n/a
18	chr7:102985197-102985247	ProgFib	skin:	n/a
19	chr7:102985197-102985247	SKMC	muscle:	n/a
20	chr7:102985197-102985247	GM12878	blood:	n/a
21	chr7:102985197-102985247	GM19239	blood:	n/a
22	chr7:102985197-102985247	GM12892	blood:	n/a
23	chr7:102985197-102985247	Hela-S3	cervix:	n/a
24	chr7:102985197-102985247	PrEC	prostate:	n/a
25	chr7:102985197-102985247	HAEpiC	amniotic membrane:	n/a
26	chr7:102985197-102985247	HUVEC	blood vessel:	n/a
27	chr7:102985197-102985247	ovcar-3	ovarian:	n/a
28	chr7:102985197-102985247	BE2_C	brain:	n/a
29	chr7:102985197-102985247	U87	brain:	n/a
30	chr7:102985197-102985247	PANC-1	pancreas:	n/a
31	chr7:102985197-102985247	NHBE	bronchial:	n/a
32	chr7:102985197-102985247	HEEpiC	esophagus:	n/a
33	chr7:102985197-102985247	HIPEpiC	eye:	n/a
34	chr7:102985197-102985247	HNPCEpiC	eye:	n/a
35	chr7:102985197-102985247	AG04450	lung:	fetal
36	chr7:102985197-102985247	NH-A	brain:	n/a
37	chr7:102985197-102985247	A549	lung:	n/a
38	chr7:102985197-102985247	HCPEpiC	choroid plexus:	n/a
39	chr7:102985197-102985247	IMR90	lung:	fetal
40	chr7:102985197-102985247	HRE	kidney:	n/a
41	chr7:102985197-102985247	T-47D	breast:	n/a
42	chr7:102985197-102985247	HRPEpiC	eye:	n/a
43	chr7:102985197-102985247	HMEC	breast:	n/a
44	chr7:102985197-102985247	HCT-116	colon:	n/a
45	chr7:102985197-102985247	AoSMC	blood vessel:	n/a
46	chr7:102985197-102985247	Jurkat	blood:	n/a
47	chr7:102985197-102985247	GM12891	blood:	n/a
48	chr7:102985197-102985247	AG09309	skin:	n/a
49	chr7:102985197-102985247	BJ	skin:	n/a
50	chr7:102985197-102985247	LNCaP	prostate:	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:102936363..102940498-chr7:102983696..102986201,5	K562	blood:
2	chr17:46125747..46126559-chr7:102984757..102985280,2	Hela-S3	cervix:
3	chr7:102937260..102939405-chr7:102983367..102989226,6	MCF-7	breast:
4	chr7:102983625..102990524-chr7:102994295..102998538,7	MCF-7	breast:
5	chr7:102935903..102938136-chr7:102983489..102985608,2	MCF-7	breast:
6	chr7:102936427..102940589-chr7:102983649..102988902,7	K562	blood:

Variant related genes	Relation type
ENSG00000235354	TF binding region
DNAJC2	TF binding region
PSMC2	TF binding region
ENSG00000235354	CpG island
DNAJC2	CpG island
PSMC2	CpG island
ENSG00000082641	Chromatin interaction
ENSG00000161057	Chromatin interaction
ENSG00000105819	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11489600	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11772383	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12667428	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12705114	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12705115	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13221892	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13228258	0.91[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3959214	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4729905	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs4729907	0.91[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs4729909	0.90[CEU][hapmap];0.81[CHB][hapmap]

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	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2074624	RP11-401L13.5	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102983200-102985600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:102983600-102985600	Active TSS	HSMM	muscle
3	chr7:102983600-102985800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:102983800-102985400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr7:102983800-102985600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr7:102983800-102985600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:102983800-102985600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr7:102983800-102985600	Active TSS	Psoas Muscle	Psoas
9	chr7:102983800-102985600	Active TSS	Right Ventricle	heart
10	chr7:102983800-102985600	Active TSS	HSMMtube	muscle
11	chr7:102983800-102985800	Active TSS	GM12878-XiMat	blood
12	chr7:102984000-102985600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr7:102984000-102985600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr7:102984000-102985600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:102984000-102985600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:102984000-102985600	Active TSS	Fetal Muscle Leg	muscle
17	chr7:102984000-102985600	Active TSS	Fetal Thymus	thymus
18	chr7:102984000-102985600	Active TSS	Right Atrium	heart
19	chr7:102984000-102985600	Active TSS	A549	lung
20	chr7:102984000-102985600	Active TSS	HMEC	breast
21	chr7:102984000-102985600	Active TSS	NHEK	skin
22	chr7:102984200-102985400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr7:102984200-102985400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:102984200-102985400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:102984200-102985400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr7:102984200-102985400	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr7:102984200-102985400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:102984200-102985400	Active TSS	Esophagus	oesophagus
29	chr7:102984200-102985400	Active TSS	Fetal Muscle Trunk	muscle
30	chr7:102984200-102985400	Active TSS	Left Ventricle	heart
31	chr7:102984200-102985400	Active TSS	Lung	lung
32	chr7:102984200-102985400	Active TSS	Pancreas	Pancrea
33	chr7:102984200-102985600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:102984200-102985600	Active TSS	Aorta	Aorta
35	chr7:102984200-102985600	Active TSS	Colonic Mucosa	Colon
36	chr7:102984200-102985600	Active TSS	Ovary	ovary
37	chr7:102984200-102985600	Active TSS	NHLF	lung
38	chr7:102984200-102985800	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr7:102984200-102985800	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr7:102984200-102985800	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr7:102984200-102985800	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr7:102984200-102985800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr7:102984200-102985800	Active TSS	Fetal Intestine Large	intestine
44	chr7:102984200-102985800	Active TSS	NHDF-Ad	bronchial
45	chr7:102984400-102985400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:102984400-102985400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr7:102984400-102985400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:102984400-102985400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:102984400-102985400	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr7:102984400-102985400	Active TSS	Primary T killer memory cells from peripheral blood	blood

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