Variant report

Variant	rs73709592
Chromosome Location	chr7:83824442-83824443
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	chr7:83823967-83824483	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF12	chr7:83824076-83824801	ECC-1	luminal epithelium:	n/a	n/a
3	ATF3	chr7:83824114-83824543	A549	lung:	n/a	n/a
4	CEBPB	chr7:83824220-83824612	Hela-S3	cervix:	n/a	n/a
5	FOXP2	chr7:83824365-83824592	SK-N-MC	brain:	n/a	n/a
6	SP1	chr7:83823789-83824683	A549	lung:	n/a	n/a
7	SIN3AK20	chr7:83824261-83824600	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr7:83824360-83824510	SAEC	small airway:	n/a	n/a
9	PBX3	chr7:83823737-83824693	SK-N-SH	brain:	n/a	n/a
10	EP300	chr7:83823831-83824861	ECC-1	luminal epithelium:	n/a	chr7:83824414-83824421 chr7:83824173-83824187
11	POLR2A	chr7:83823496-83824695	H1-neurons	neurons:	n/a	n/a
12	YY1	chr7:83824195-83824644	H1-hESC	embryonic stem cell:	n/a	n/a
13	BACH1	chr7:83824234-83824504	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr7:83823778-83824635	Hela-S3	cervix:	n/a	n/a
15	SIN3AK20	chr7:83824277-83824626	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr7:83823766-83824641	SK-N-SH	brain:	n/a	n/a
17	KAP1	chr7:83824271-83824715	U2OS	brain:	n/a	n/a
18	MAX	chr7:83823714-83824823	ECC-1	luminal epithelium:	n/a	chr7:83824042-83824051
19	REST	chr7:83824209-83824624	SK-N-SH	brain:	n/a	chr7:83824375-83824393
20	JUND	chr7:83824085-83824610	A549	lung:	n/a	n/a
21	MYC	chr7:83823393-83824532	MCF10A-Er-Src	breast:	n/a	chr7:83824042-83824051
22	BHLHE40	chr7:83824279-83824470	GM12878	blood:	n/a	n/a
23	POLR2A	chr7:83824115-83824583	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr7:83824300-83824450	AG04450	lung:	n/a	n/a
25	WRNIP1	chr7:83824374-83824533	GM12878	blood:	n/a	n/a
26	MXI1	chr7:83824244-83824633	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr7:83824096-83824711	PANC-1	pancreas:	n/a	n/a
28	CTCF	chr7:83824320-83824470	HPAF	blood vessel:	n/a	n/a
29	MAX	chr7:83823807-83824606	NB4	blood:	n/a	chr7:83824042-83824051
30	MAX	chr7:83824123-83824788	A549	lung:	n/a	n/a
31	CTCF	chr7:83824300-83824450	AG09319	gingival:	n/a	n/a
32	MAX	chr7:83823742-83824748	SK-N-SH	brain:	n/a	chr7:83824042-83824051
33	TCF7L2	chr7:83824020-83824638	Hela-S3	cervix:	n/a	chr7:83824225-83824241 chr7:83824225-83824241
34	TAF1	chr7:83824346-83824470	PFSK-1	brain:	n/a	n/a
35	ZNF263	chr7:83823820-83825071	HEK293-T-REx	kidney:	n/a	chr7:83824831-83824840
36	RAD21	chr7:83824095-83824596	A549	lung:	n/a	n/a
37	JUND	chr7:83823962-83824632	Hela-S3	cervix:	n/a	n/a
38	SP1	chr7:83823942-83824672	A549	lung:	n/a	n/a
39	RAD21	chr7:83823666-83824893	IMR90	lung:	n/a	n/a
40	CHD1	chr7:83823174-83826140	IMR90	lung:	n/a	n/a
41	CTCF	chr7:83824340-83824490	AoAF	blood vessel:	n/a	n/a
42	STAT3	chr7:83824204-83824477	MCF10A-Er-Src	breast:	n/a	n/a
43	RAD21	chr7:83823785-83824649	SK-N-SH_RA	brain:	n/a	n/a
44	CTCF	chr7:83824400-83824550	GM12865	blood:	n/a	n/a
45	TCF12	chr7:83824057-83824834	ECC-1	luminal epithelium:	n/a	n/a
46	MAX	chr7:83823913-83824597	H1-hESC	embryonic stem cell:	n/a	chr7:83824042-83824051
47	TAF1	chr7:83824283-83824482	GM12891	blood:	n/a	n/a
48	TBP	chr7:83824334-83824554	H1-hESC	embryonic stem cell:	n/a	n/a
49	TCF7L2	chr7:83823815-83824623	PANC-1	pancreas:	n/a	chr7:83824225-83824241 chr7:83824225-83824241
50	MAX	chr7:83823719-83824733	SK-N-SH	brain:	n/a	chr7:83824042-83824051

Variant related genes	Relation type
SEMA3A	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11971838	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11976488	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11981143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11982044	1.00[ASN][1000 genomes]
rs11982456	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28631483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58513095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61194772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73709587	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73709588	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73709589	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73709590	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73709595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73709602	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73712705	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv888629	chr7:83722691-83896025	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1017884	chr7:83724138-83972995	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538995	chr7:83724138-83972995	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83819400-83825800	Active TSS	Stomach Smooth Muscle	stomach
2	chr7:83819400-83826000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:83819600-83824800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:83819600-83826000	Active TSS	NHLF	lung
5	chr7:83820000-83825800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:83820600-83824600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:83820600-83825600	Active TSS	Fetal Intestine Large	intestine
8	chr7:83820600-83825800	Active TSS	Fetal Stomach	stomach
9	chr7:83820600-83826000	Active TSS	Colon Smooth Muscle	Colon
10	chr7:83820600-83826000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr7:83820600-83826000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr7:83820800-83824600	Active TSS	Fetal Brain Female	brain
13	chr7:83820800-83825000	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr7:83820800-83825600	Active TSS	Fetal Muscle Leg	muscle
15	chr7:83820800-83826000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr7:83820800-83826000	Active TSS	Rectal Smooth Muscle	rectum
17	chr7:83820800-83826200	Active TSS	NHDF-Ad	bronchial
18	chr7:83821000-83824600	Active TSS	NH-A	brain
19	chr7:83821000-83824800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:83821000-83825600	Active TSS	Brain Germinal Matrix	brain
21	chr7:83821000-83826000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:83821000-83826200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:83821200-83824600	Active TSS	H1 Cell Line	embryonic stem cell
24	chr7:83821200-83826000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:83821400-83824600	Active TSS	HMEC	breast
26	chr7:83821400-83824800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:83821400-83825800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:83821400-83825800	Active TSS	Fetal Kidney	kidney
29	chr7:83821600-83825800	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr7:83821800-83824600	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr7:83821800-83824800	Active TSS	A549	lung
32	chr7:83821800-83825800	Active TSS	H9 Cell Line	embryonic stem cell
33	chr7:83821800-83825800	Active TSS	Fetal Lung	lung
34	chr7:83822000-83824600	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr7:83822000-83824600	Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr7:83822000-83824600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:83822000-83824800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:83822000-83824800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:83822200-83824800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:83822400-83824600	Active TSS	Fetal Heart	heart
41	chr7:83822400-83824600	Active TSS	Osteobl	bone
42	chr7:83822400-83824800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr7:83822400-83825000	Active TSS	Fetal Intestine Small	intestine
44	chr7:83822400-83825800	Active TSS	Brain Cingulate Gyrus	brain
45	chr7:83822600-83824600	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr7:83822600-83825800	Active TSS	Fetal Muscle Trunk	muscle
47	chr7:83822600-83825800	Active TSS	Right Atrium	heart
48	chr7:83822600-83826000	Active TSS	Brain Angular Gyrus	brain
49	chr7:83822600-83826000	Active TSS	Brain Hippocampus Middle	brain
50	chr7:83822800-83824600	Active TSS	Fetal Brain Male	brain

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