Variant report

Variant	rs28411396
Chromosome Location	chr9:104295961-104295962
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	GABPA	chr9:104295762-104296315	H1-hESC	embryonic stem cell:	n/a	chr9:104295974-104295988
2	SIX5	chr9:104295718-104296312	A549	lung:	n/a	n/a
3	SP1	chr9:104295556-104296266	GM12878	blood:	n/a	chr9:104296121-104296130 chr9:104296120-104296132 chr9:104296120-104296132 chr9:104296122-104296131 chr9:104296121-104296135
4	POLR2A	chr9:104295641-104296507	MCF-7	breast:	n/a	n/a
5	PBX3	chr9:104295419-104296455	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr9:104295638-104296589	Hela-S3	cervix:	n/a	n/a
7	ARID3A	chr9:104295942-104296283	K562	blood:	n/a	n/a
8	POLR2A	chr9:104295820-104296445	GM12878	blood:	n/a	n/a
9	SPI1	chr9:104295806-104296311	HL-60	blood:	n/a	chr9:104296086-104296099 chr9:104295838-104295851 chr9:104296085-104296098 chr9:104295839-104295852 chr9:104295841-104295850
10	BRCA1	chr9:104295927-104296269	HepG2	liver:	n/a	n/a
11	TBL1XR1	chr9:104295387-104296369	GM12878	blood:	n/a	n/a
12	POLR2A	chr9:104295579-104296494	HepG2	liver:	n/a	n/a
13	POLR2A	chr9:104295924-104296324	PANC-1	pancreas:	n/a	n/a
14	GTF2F1	chr9:104295621-104296746	Hela-S3	cervix:	n/a	n/a
15	PBX3	chr9:104295585-104296052	A549	lung:	n/a	n/a
16	MAX	chr9:104295618-104296583	SK-N-SH	brain:	n/a	n/a
17	MAX	chr9:104295689-104296478	Hela-S3	cervix:	n/a	n/a
18	EP300	chr9:104295617-104296272	HepG2	liver:	n/a	chr9:104296087-104296096 chr9:104296131-104296138 chr9:104296094-104296108
19	ZBTB7A	chr9:104295901-104296088	K562	blood:	n/a	n/a
20	RCOR1	chr9:104295811-104296539	Hela-S3	cervix:	n/a	n/a
21	GABPA	chr9:104295442-104296711	SK-N-SH	brain:	n/a	chr9:104295974-104295988
22	POLR2A	chr9:104295709-104296411	HEK293	kidney:	n/a	n/a
23	CEBPB	chr9:104295819-104296267	ECC-1	luminal epithelium:	n/a	n/a
24	TCF12	chr9:104295512-104296612	A549	lung:	n/a	n/a
25	POLR2A	chr9:104295714-104296450	ECC-1	luminal epithelium:	n/a	n/a
26	WRNIP1	chr9:104295494-104296768	GM12878	blood:	n/a	n/a
27	MXI1	chr9:104295768-104296282	H1-hESC	embryonic stem cell:	n/a	chr9:104295988-104296003
28	RFX5	chr9:104295710-104296448	HepG2	liver:	n/a	chr9:104295988-104295997 chr9:104295985-104295999
29	MYC	chr9:104295345-104296561	K562	blood:	n/a	n/a
30	MYC	chr9:104295400-104296537	K562	blood:	n/a	n/a
31	CREB1	chr9:104295587-104296315	K562	blood:	n/a	n/a
32	CREB1	chr9:104295715-104296224	A549	lung:	n/a	n/a
33	SP2	chr9:104295493-104296293	HepG2	liver:	n/a	n/a
34	POLR2A	chr9:104295407-104296609	H1-hESC	embryonic stem cell:	n/a	n/a
35	CREB1	chr9:104295530-104296403	GM12878	blood:	n/a	n/a
36	POLR2A	chr9:104295572-104296630	Hela-S3	cervix:	n/a	n/a
37	CHD2	chr9:104295631-104296545	K562	blood:	n/a	n/a
38	POLR2A	chr9:104295883-104296405	MCF-7	breast:	n/a	n/a
39	POLR2A	chr9:104295522-104296459	MCF10A-Er-Src	breast:	n/a	n/a
40	TBP	chr9:104295617-104296395	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF1	chr9:104295931-104296267	PFSK-1	brain:	n/a	n/a
42	GABPA	chr9:104295813-104296263	Hela-S3	cervix:	n/a	chr9:104295974-104295988
43	TCF7L2	chr9:104295869-104296513	HCT-116	colon:	n/a	n/a
44	REST	chr9:104295267-104296803	H1-neurons	neurons:	n/a	chr9:104296111-104296124
45	ELF1	chr9:104295667-104296301	HepG2	liver:	n/a	chr9:104296128-104296139 chr9:104296129-104296138
46	NFIC	chr9:104295776-104296466	HepG2	liver:	n/a	n/a
47	PBX3	chr9:104295384-104296380	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr9:104295792-104296416	GM12878	blood:	n/a	n/a
49	FOXP2	chr9:104295903-104296208	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr9:104295445-104296794	GM19099	blood:	n/a	n/a

Variant related genes	Relation type
RNF20	TF binding region
TMEM246	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11793946	1.00[ASN][1000 genomes]
rs13287159	1.00[AFR][1000 genomes]
rs13289614	1.00[AFR][1000 genomes]
rs13292935	1.00[AFR][1000 genomes]
rs16920437	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16920441	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16920477	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16920487	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16920497	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16920501	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1929483	0.81[ASN][1000 genomes]
rs2181561	1.00[AFR][1000 genomes]
rs2417270	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2417271	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35320813	1.00[AFR][1000 genomes]
rs35698290	1.00[AFR][1000 genomes]
rs35778437	1.00[AFR][1000 genomes]
rs36074111	1.00[AFR][1000 genomes]
rs3813523	0.81[ASN][1000 genomes]
rs41282149	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs41282153	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs41282155	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs41306471	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs45587135	0.94[ASN][1000 genomes]
rs56742090	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs56998622	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59048832	0.94[AMR][1000 genomes]
rs61437380	0.94[AMR][1000 genomes]
rs62000403	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62575836	1.00[ASN][1000 genomes]
rs62575837	1.00[ASN][1000 genomes]
rs71509736	1.00[AFR][1000 genomes]
rs72745305	1.00[ASN][1000 genomes]
rs73659558	0.89[AMR][1000 genomes]
rs7859863	0.88[ASN][1000 genomes]
rs7872953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873986	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9792479	0.91[AMR][1000 genomes]
rs9792648	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs989900	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs989901	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv893627	chr9:104268342-104334333	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104295000-104296200	Active TSS	Fetal Lung	lung
2	chr9:104295200-104296400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr9:104295200-104296600	Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr9:104295200-104296800	Active TSS	Brain Substantia Nigra	brain
5	chr9:104295200-104296800	Active TSS	Colon Smooth Muscle	Colon
6	chr9:104295200-104297000	Active TSS	Fetal Brain Female	brain
7	chr9:104295200-104297200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr9:104295200-104297200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:104295200-104297200	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr9:104295200-104297200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr9:104295200-104297200	Active TSS	Stomach Smooth Muscle	stomach
12	chr9:104295200-104297200	Active TSS	K562	blood
13	chr9:104295400-104296000	Flanking Active TSS	Placenta	Placenta
14	chr9:104295400-104296200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:104295400-104296400	Active TSS	Brain Cingulate Gyrus	brain
16	chr9:104295400-104296400	Active TSS	Fetal Thymus	thymus
17	chr9:104295400-104296400	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr9:104295400-104296600	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr9:104295400-104296600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:104295400-104296600	Active TSS	Pancreas	Pancrea
21	chr9:104295400-104296600	Active TSS	Placenta Amnion	Placenta Amnion
22	chr9:104295400-104296800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr9:104295400-104296800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:104295400-104296800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:104295400-104296800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:104295400-104296800	Active TSS	Colonic Mucosa	Colon
27	chr9:104295400-104296800	Active TSS	Esophagus	oesophagus
28	chr9:104295400-104296800	Active TSS	Left Ventricle	heart
29	chr9:104295400-104296800	Active TSS	Lung	lung
30	chr9:104295400-104297000	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr9:104295400-104297000	Active TSS	H1 Cell Line	embryonic stem cell
32	chr9:104295400-104297000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr9:104295400-104297000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:104295400-104297000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:104295400-104297000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:104295400-104297000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:104295400-104297000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr9:104295400-104297000	Active TSS	Aorta	Aorta
39	chr9:104295400-104297000	Active TSS	Fetal Intestine Large	intestine
40	chr9:104295400-104297000	Active TSS	Fetal Muscle Trunk	muscle
41	chr9:104295400-104297000	Active TSS	Fetal Stomach	stomach
42	chr9:104295400-104297000	Active TSS	Ovary	ovary
43	chr9:104295400-104297000	Active TSS	Psoas Muscle	Psoas
44	chr9:104295400-104297000	Active TSS	Rectal Smooth Muscle	rectum
45	chr9:104295400-104297000	Active TSS	Right Atrium	heart
46	chr9:104295400-104297000	Active TSS	A549	lung
47	chr9:104295400-104297200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:104295400-104297200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:104295400-104297200	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr9:104295400-104297200	Active TSS	Right Ventricle	heart

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