Variant report

Variant	rs6716846
Chromosome Location	chr2:73316999-73317000
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	FOXA1	chr2:73316790-73317111	T-47D	breast:	n/a	n/a
2	FOSL2	chr2:73316681-73317326	A549	lung:	n/a	n/a
3	SIN3AK20	chr2:73316792-73317231	SK-N-SH	brain:	n/a	n/a
4	FOS	chr2:73316741-73317231	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr2:73316784-73317188	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA3	chr2:73316563-73317472	SK-N-SH	brain:	n/a	n/a
7	SP1	chr2:73316783-73317268	A549	lung:	n/a	n/a
8	POLR2A	chr2:73316421-73317109	IMR90	lung:	n/a	n/a
9	STAT3	chr2:73316788-73317176	MCF10A-Er-Src	breast:	n/a	chr2:73316803-73316815
10	GTF2F1	chr2:73316745-73317354	Hela-S3	cervix:	n/a	n/a
11	JUND	chr2:73316440-73317409	SK-N-SH	brain:	n/a	chr2:73317055-73317066
12	TCF12	chr2:73316465-73317355	SK-N-SH	brain:	n/a	n/a
13	MAX	chr2:73316788-73317081	Hela-S3	cervix:	n/a	n/a
14	ZNF143	chr2:73316906-73317237	Hela-S3	cervix:	n/a	n/a
15	RCOR1	chr2:73316821-73317089	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr2:73316757-73317086	HUVEC	blood vessel:	n/a	n/a
17	MYC	chr2:73316963-73317092	HUVEC	blood vessel:	n/a	n/a
18	JUN	chr2:73316818-73317152	HepG2	liver:	n/a	n/a
19	RAD21	chr2:73316677-73317190	IMR90	lung:	n/a	n/a
20	JUND	chr2:73316828-73317154	A549	lung:	n/a	chr2:73317055-73317066
21	MYC	chr2:73316801-73317145	MCF10A-Er-Src	breast:	n/a	n/a
22	TEAD4	chr2:73316694-73317286	ECC-1	luminal epithelium:	n/a	n/a
23	CEBPB	chr2:73316768-73317301	Hela-S3	cervix:	n/a	n/a
24	FOS	chr2:73316753-73317256	HUVEC	blood vessel:	n/a	n/a
25	FOS	chr2:73316775-73317233	MCF10A-Er-Src	breast:	n/a	n/a
26	GATA3	chr2:73316828-73317259	T-47D	breast:	n/a	n/a
27	TAF1	chr2:73316683-73317050	SK-N-SH	brain:	n/a	n/a
28	GATA3	chr2:73316603-73317372	SK-N-SH	brain:	n/a	n/a
29	NFIC	chr2:73316583-73317279	SK-N-SH	brain:	n/a	n/a
30	PBX3	chr2:73316621-73317355	SK-N-SH	brain:	n/a	n/a
31	JUND	chr2:73316538-73317296	SK-N-SH	brain:	n/a	chr2:73317055-73317066
32	E2F4	chr2:73316817-73317102	MCF10A-Er-Src	breast:	n/a	n/a
33	JUND	chr2:73316671-73317245	A549	lung:	n/a	chr2:73317055-73317066
34	RAD21	chr2:73316750-73317080	SK-N-SH_RA	brain:	n/a	n/a
35	SIN3AK20	chr2:73316903-73317110	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr2:73316509-73317255	SK-N-SH	brain:	n/a	n/a
37	FOSL2	chr2:73316842-73317148	A549	lung:	n/a	n/a
38	CHD2	chr2:73316864-73317182	Hela-S3	cervix:	n/a	n/a
39	REST	chr2:73316610-73317138	SK-N-SH	brain:	n/a	chr2:73316813-73316826
40	JUN	chr2:73316716-73317300	Hela-S3	cervix:	n/a	n/a
41	JUND	chr2:73316946-73317097	HepG2	liver:	n/a	chr2:73317055-73317066
42	STAT3	chr2:73316957-73317004	MCF10A-Er-Src	breast:	n/a	n/a
43	RAD21	chr2:73316790-73317099	Hela-S3	cervix:	n/a	n/a
44	SMC3	chr2:73316686-73317144	Hela-S3	cervix:	n/a	n/a
45	STAT3	chr2:73316791-73317183	MCF10A-Er-Src	breast:	n/a	chr2:73316803-73316815
46	STAT3	chr2:73316807-73317220	MCF10A-Er-Src	breast:	n/a	n/a
47	GABPA	chr2:73316799-73317214	A549	lung:	n/a	n/a
48	POLR2A	chr2:73316784-73317132	HCT-116	colon:	n/a	n/a
49	MYC	chr2:73316862-73317114	MCF10A-Er-Src	breast:	n/a	n/a
50	FOXA2	chr2:73316768-73317175	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73300909..73302911-chr2:73316133..73317647,2	K562	blood:
2	chr2:73300396..73302911-chr2:73315000..73317633,2	K562	blood:

Variant related genes	Relation type
RAB11FIP5	TF binding region
ENSG00000144040	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1046183	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13404068	0.92[ASN][1000 genomes]
rs2421099	0.94[ASN][1000 genomes]
rs56931614	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56992198	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57875548	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58469852	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58649746	0.85[ASN][1000 genomes]
rs58659495	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59802755	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60341789	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs67421457	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	nsv1006801	chr2:73305056-73431711	Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73299400-73318200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:73299400-73318400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:73299600-73319400	Weak transcription	K562	blood
4	chr2:73300000-73319200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:73303000-73328600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:73303200-73320600	Weak transcription	Psoas Muscle	Psoas
7	chr2:73303400-73320000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:73309200-73319400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:73313000-73317400	Genic enhancers	Spleen	Spleen
10	chr2:73313000-73319000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:73313200-73319000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:73313200-73320000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:73313200-73327200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:73315200-73317600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:73315200-73319000	Enhancers	Fetal Heart	heart
16	chr2:73315400-73318400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:73315400-73319000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:73315600-73318600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:73315600-73319600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:73315600-73330400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:73315600-73338000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:73315800-73317200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:73315800-73317400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:73315800-73317600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:73315800-73317800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:73315800-73318200	Weak transcription	Liver	Liver
27	chr2:73315800-73318600	Enhancers	HMEC	breast
28	chr2:73315800-73319000	Weak transcription	Brain Anterior Caudate	brain
29	chr2:73315800-73319800	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:73315800-73320000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:73316000-73317400	Weak transcription	Small Intestine	intestine
32	chr2:73316000-73318400	Weak transcription	Brain Angular Gyrus	brain
33	chr2:73316000-73318400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:73316000-73318800	Enhancers	NHDF-Ad	bronchial
35	chr2:73316000-73319600	Enhancers	HSMMtube	muscle
36	chr2:73316000-73320600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:73316000-73321000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:73316000-73326600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:73316200-73317200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr2:73316200-73317400	Enhancers	Lung	lung
41	chr2:73316200-73317400	Enhancers	Right Atrium	heart
42	chr2:73316200-73317800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:73316200-73317800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:73316200-73317800	Enhancers	Left Ventricle	heart
45	chr2:73316200-73317800	Enhancers	Rectal Smooth Muscle	rectum
46	chr2:73316200-73317800	Enhancers	HUVEC	blood vessel
47	chr2:73316200-73318600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:73316200-73319000	Weak transcription	Colonic Mucosa	Colon
49	chr2:73316200-73320200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:73316200-73320600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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