Variant report

Variant	rs72825789
Chromosome Location	chr2:99346336-99346337
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	JUND	chr2:99346154-99346499	HepG2	liver:	n/a	n/a
2	JUN	chr2:99346155-99346661	HepG2	liver:	n/a	n/a
3	MBD4	chr2:99346220-99346837	HepG2	liver:	n/a	n/a
4	MYC	chr2:99346019-99347403	NB4	blood:	n/a	chr2:99347002-99347012
5	CEBPB	chr2:99346243-99346870	HepG2	liver:	n/a	n/a
6	MXI1	chr2:99346145-99347305	SK-N-SH	brain:	n/a	chr2:99347009-99347018
7	MXI1	chr2:99346332-99348316	HepG2	liver:	n/a	chr2:99347009-99347018
8	POLR2A	chr2:99346093-99346938	HUVEC	blood vessel:	n/a	n/a
9	MXI1	chr2:99346175-99346957	GM12878	blood:	n/a	n/a
10	MBD4	chr2:99346070-99346883	HepG2	liver:	n/a	n/a
11	MAX	chr2:99346071-99347068	NB4	blood:	n/a	chr2:99347002-99347012
12	POLR2A	chr2:99346112-99346425	K562	blood:	n/a	n/a
13	REST	chr2:99346240-99347372	H1-neurons	neurons:	n/a	chr2:99347087-99347105 chr2:99347069-99347078 chr2:99347210-99347223 chr2:99347050-99347060 chr2:99347072-99347085 chr2:99347322-99347332 chr2:99346967-99346980

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

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

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10496330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1877905	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59313126	0.86[EUR][1000 genomes]
rs59989465	0.86[EUR][1000 genomes]
rs72825777	0.84[EUR][1000 genomes]
rs72825780	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72825782	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72825784	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72825790	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825800	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72825801	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72827704	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72827705	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72827707	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72827708	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72827713	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72827717	0.93[EUR][1000 genomes]
rs72827722	0.93[EUR][1000 genomes]
rs72827724	0.93[EUR][1000 genomes]
rs72827727	0.86[EUR][1000 genomes]
rs72827729	0.86[EUR][1000 genomes]
rs72827731	0.86[EUR][1000 genomes]
rs72827732	0.86[EUR][1000 genomes]
rs72827733	0.86[EUR][1000 genomes]
rs72827734	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99326400-99346400	Weak transcription	Fetal Muscle Leg	muscle
2	chr2:99335200-99346600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:99340200-99346600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:99340200-99346600	Weak transcription	Esophagus	oesophagus
5	chr2:99342800-99346800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr2:99343000-99346600	Weak transcription	Gastric	stomach
7	chr2:99343800-99346800	Flanking Active TSS	Dnd41	blood
8	chr2:99344200-99348400	Active TSS	Primary T cells fromperipheralblood	blood
9	chr2:99344600-99346600	Weak transcription	Spleen	Spleen
10	chr2:99344600-99347000	Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr2:99344600-99348600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:99344800-99348600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr2:99345000-99347000	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr2:99345000-99348800	Active TSS	Duodenum Mucosa	Duodenum
15	chr2:99345200-99346600	Flanking Active TSS	HUVEC	blood vessel
16	chr2:99345200-99348400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr2:99345400-99348400	Active TSS	Primary T cells from cord blood	blood
18	chr2:99345600-99346400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:99345600-99346400	Active TSS	Adipose Nuclei	Adipose
20	chr2:99345600-99347000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr2:99345600-99347000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:99345600-99348400	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr2:99345600-99348400	Active TSS	Fetal Intestine Large	intestine
24	chr2:99345600-99349200	Active TSS	Colonic Mucosa	Colon
25	chr2:99345800-99346800	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr2:99345800-99347000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:99345800-99348200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:99345800-99348200	Active TSS	Brain Anterior Caudate	brain
29	chr2:99345800-99348200	Active TSS	Stomach Smooth Muscle	stomach
30	chr2:99345800-99348400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:99345800-99348400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:99345800-99348400	Active TSS	Ovary	ovary
33	chr2:99345800-99348400	Active TSS	Psoas Muscle	Psoas
34	chr2:99345800-99348400	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr2:99345800-99348400	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr2:99345800-99348400	Active TSS	Small Intestine	intestine
37	chr2:99345800-99348600	Active TSS	Right Atrium	heart
38	chr2:99345800-99348800	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr2:99345800-99348800	Active TSS	Fetal Intestine Small	intestine
40	chr2:99345800-99348800	Active TSS	Right Ventricle	heart
41	chr2:99345800-99349400	Active TSS	Pancreas	Pancrea
42	chr2:99346000-99346400	Enhancers	Primary B cells from peripheral blood	blood
43	chr2:99346000-99346400	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr2:99346000-99346400	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr2:99346000-99346400	Enhancers	Stomach Mucosa	stomach
46	chr2:99346000-99346600	Bivalent/Poised TSS	Fetal Brain Male	brain
47	chr2:99346000-99346800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:99346000-99346800	Flanking Active TSS	Fetal Thymus	thymus
49	chr2:99346000-99347000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:99346000-99347000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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