Variant report

Variant	rs5008045
Chromosome Location	chr2:99347699-99347700
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	MAX	chr2:99347672-99348090	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:99347686-99347931	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:99346578-99349177	HepG2	liver:	n/a	n/a
4	MAX	chr2:99347638-99347989	ECC-1	luminal epithelium:	n/a	n/a
5	JUND	chr2:99347660-99347873	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:99347671-99347983	GM12892	blood:	n/a	n/a
7	POLR2A	chr2:99347671-99348067	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr2:99347358-99348371	Raji	blood:	n/a	n/a
9	YY1	chr2:99347576-99348188	GM12892	blood:	n/a	chr2:99347846-99347860 chr2:99347866-99347877 chr2:99347750-99347759 chr2:99347866-99347875
10	MAX	chr2:99346545-99348819	HepG2	liver:	n/a	chr2:99347002-99347012
11	MAX	chr2:99347684-99348066	H1-hESC	embryonic stem cell:	n/a	n/a
12	CREB1	chr2:99346553-99348804	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:99346628-99347992	NB4	blood:	n/a	n/a
14	E2F6	chr2:99347630-99348113	A549	lung:	n/a	chr2:99347866-99347875
15	MAX	chr2:99347669-99348361	MCF-7	breast:	n/a	n/a
16	MAX	chr2:99347461-99348181	A549	lung:	n/a	n/a
17	CHD2	chr2:99347694-99348352	GM12878	blood:	n/a	n/a
18	RAD21	chr2:99347182-99348174	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:99347372-99347990	HCT-116	colon:	n/a	n/a
20	PML	chr2:99347643-99348889	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:99347688-99347807	H1-hESC	embryonic stem cell:	n/a	n/a
22	PBX3	chr2:99347651-99348008	SK-N-SH	brain:	n/a	chr2:99347726-99347746 chr2:99347914-99347934
23	POLR2A	chr2:99347282-99348244	GM19193	blood:	n/a	n/a
24	TAF1	chr2:99347648-99348042	ECC-1	luminal epithelium:	n/a	n/a
25	TAF1	chr2:99347667-99347991	H1-neurons	neurons:	n/a	n/a
26	POLR2A	chr2:99347654-99347956	A549	lung:	n/a	n/a
27	POLR2A	chr2:99347192-99348312	GM19099	blood:	n/a	n/a
28	HNF4G	chr2:99347673-99347958	HepG2	liver:	n/a	n/a
29	REST	chr2:99347479-99348546	H1-neurons	neurons:	n/a	chr2:99347912-99347925 chr2:99347991-99348004 chr2:99348082-99348095 chr2:99347952-99347965
30	RCOR1	chr2:99347694-99348703	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:99347505-99348395	HL-60	blood:	n/a	n/a
32	POLR2A	chr2:99347659-99348022	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:99346670-99348244	MCF-7	breast:	n/a	n/a
34	HEY1	chr2:99347663-99349341	HepG2	liver:	n/a	chr2:99348124-99348139 chr2:99348047-99348062
35	MYBL2	chr2:99347589-99348850	HepG2	liver:	n/a	n/a
36	CEBPD	chr2:99347639-99347979	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:99346782-99348278	HUVEC	blood vessel:	n/a	n/a
38	YY1	chr2:99347480-99348206	HepG2	liver:	n/a	chr2:99347846-99347860 chr2:99347866-99347877 chr2:99347750-99347759 chr2:99347866-99347875
39	MAZ	chr2:99346625-99348050	HepG2	liver:	n/a	chr2:99347002-99347012
40	POLR2A	chr2:99347661-99347859	A549	lung:	n/a	n/a
41	MAX	chr2:99347671-99348059	H1-hESC	embryonic stem cell:	n/a	n/a
42	SP1	chr2:99347626-99347902	GM12878	blood:	n/a	n/a
43	MYC	chr2:99347505-99347993	MCF-7	breast:	n/a	n/a
44	TBP	chr2:99347675-99348707	HepG2	liver:	n/a	n/a
45	YY1	chr2:99347609-99347969	GM12891	blood:	n/a	chr2:99347846-99347860 chr2:99347866-99347877 chr2:99347750-99347759 chr2:99347866-99347875
46	POLR2A	chr2:99347638-99347938	A549	lung:	n/a	n/a
47	HDAC2	chr2:99347610-99348350	HepG2	liver:	n/a	chr2:99348295-99348304
48	MXI1	chr2:99346332-99348316	HepG2	liver:	n/a	chr2:99347009-99347018
49	RUNX3	chr2:99347695-99348015	GM12878	blood:	n/a	n/a
50	TAF1	chr2:99346611-99348212	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:99221557..99223102-chr2:99346482..99348239,2	MCF-7	breast:
2	chr2:99343338..99345259-chr2:99346373..99348700,3	MCF-7	breast:
3	chr2:99345360..99347894-chr2:99396622..99399352,2	MCF-7	breast:
4	chr2:99342514..99344879-chr2:99346177..99348798,2	K562	blood:
5	chr2:99344922..99348721-chr2:99382903..99389092,6	MCF-7	breast:
6	chr2:99342228..99344879-chr2:99346177..99348874,2	K562	blood:
7	chr2:99345368..99349321-chr2:99385005..99390572,6	MCF-7	breast:

Variant related genes	Relation type
MGAT4A	TF binding region
ENSG00000226791	Chromatin interaction
ENSG00000201070	Chromatin interaction
ENSG00000071073	Chromatin interaction
ENSG00000183513	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10177696	0.82[EUR][1000 genomes]
rs10194177	0.81[EUR][1000 genomes]
rs12477450	0.82[EUR][1000 genomes]
rs1514916	0.82[EUR][1000 genomes]
rs41445250	0.82[EUR][1000 genomes]
rs58666702	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv535836	chr2:99329084-99353519	Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535837	chr2:99329084-99358356	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535838	chr2:99335416-99358356	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3377346	chr2:99345945-99348493	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv3405477	chr2:99346570-99349018	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3338485	chr2:99347070-99348418	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr2:99344200-99348400	Active TSS	Primary T cells fromperipheralblood	blood
2	chr2:99344600-99348600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:99344800-99348600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr2:99345000-99348800	Active TSS	Duodenum Mucosa	Duodenum
5	chr2:99345200-99348400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:99345400-99348400	Active TSS	Primary T cells from cord blood	blood
7	chr2:99345600-99348400	Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr2:99345600-99348400	Active TSS	Fetal Intestine Large	intestine
9	chr2:99345600-99349200	Active TSS	Colonic Mucosa	Colon
10	chr2:99345800-99348200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:99345800-99348200	Active TSS	Brain Anterior Caudate	brain
12	chr2:99345800-99348200	Active TSS	Stomach Smooth Muscle	stomach
13	chr2:99345800-99348400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:99345800-99348400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:99345800-99348400	Active TSS	Ovary	ovary
16	chr2:99345800-99348400	Active TSS	Psoas Muscle	Psoas
17	chr2:99345800-99348400	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr2:99345800-99348400	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr2:99345800-99348400	Active TSS	Small Intestine	intestine
20	chr2:99345800-99348600	Active TSS	Right Atrium	heart
21	chr2:99345800-99348800	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr2:99345800-99348800	Active TSS	Fetal Intestine Small	intestine
23	chr2:99345800-99348800	Active TSS	Right Ventricle	heart
24	chr2:99345800-99349400	Active TSS	Pancreas	Pancrea
25	chr2:99346000-99348200	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr2:99346000-99348400	Active TSS	Brain Hippocampus Middle	brain
27	chr2:99346000-99348400	Active TSS	Brain Substantia Nigra	brain
28	chr2:99346000-99348600	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr2:99346000-99348600	Bivalent/Poised TSS	HepG2	liver
30	chr2:99346200-99348200	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr2:99346200-99348400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr2:99346200-99348600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:99346200-99348600	Active TSS	Aorta	Aorta
34	chr2:99346200-99348800	Active TSS	Left Ventricle	heart
35	chr2:99346200-99348800	Active TSS	Lung	lung
36	chr2:99346200-99348800	Active TSS	Thymus	Thymus
37	chr2:99346400-99348200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
38	chr2:99346400-99348200	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr2:99346400-99348200	Active TSS	Brain Cingulate Gyrus	brain
40	chr2:99346400-99348200	Active TSS	Stomach Mucosa	stomach
41	chr2:99346400-99348400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:99346400-99348400	Active TSS	Brain Angular Gyrus	brain
43	chr2:99346400-99348600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
44	chr2:99346400-99348600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
45	chr2:99346600-99348000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr2:99346600-99348000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:99346600-99348000	Active TSS	HUVEC	blood vessel
48	chr2:99346600-99348200	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr2:99346600-99348200	Bivalent/Poised TSS	Fetal Stomach	stomach
50	chr2:99346600-99348200	Active TSS	Rectal Smooth Muscle	rectum

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