Variant report

Variant	rs376530906
Chromosome Location	chr2:99348335-99348336
allele	C/G
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	chr2:99346578-99349177	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:99347358-99348371	Raji	blood:	n/a	n/a
3	MAX	chr2:99346545-99348819	HepG2	liver:	n/a	chr2:99347002-99347012
4	CREB1	chr2:99346553-99348804	HepG2	liver:	n/a	n/a
5	MAX	chr2:99347669-99348361	MCF-7	breast:	n/a	n/a
6	CHD2	chr2:99347694-99348352	GM12878	blood:	n/a	n/a
7	PML	chr2:99347643-99348889	GM12878	blood:	n/a	n/a
8	MXI1	chr2:99347795-99348386	GM12878	blood:	n/a	n/a
9	REST	chr2:99347479-99348546	H1-neurons	neurons:	n/a	chr2:99347912-99347925 chr2:99347991-99348004 chr2:99348082-99348095 chr2:99347952-99347965
10	TEAD4	chr2:99348159-99349061	HepG2	liver:	n/a	n/a
11	CHD2	chr2:99347720-99348370	HepG2	liver:	n/a	n/a
12	RCOR1	chr2:99347694-99348703	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:99347505-99348395	HL-60	blood:	n/a	n/a
14	HEY1	chr2:99347663-99349341	HepG2	liver:	n/a	chr2:99348124-99348139 chr2:99348047-99348062
15	MYBL2	chr2:99347589-99348850	HepG2	liver:	n/a	n/a
16	NFIC	chr2:99348106-99348797	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:99347708-99349152	HepG2	liver:	n/a	n/a
18	TBP	chr2:99347675-99348707	HepG2	liver:	n/a	n/a
19	EP300	chr2:99347755-99348723	HepG2	liver:	n/a	chr2:99347861-99347877 chr2:99347844-99347860 chr2:99347866-99347882
20	HDAC2	chr2:99347610-99348350	HepG2	liver:	n/a	chr2:99348295-99348304
21	TCF7L2	chr2:99347808-99348495	HEK293	kidney:	n/a	chr2:99348328-99348344 chr2:99348331-99348340 chr2:99348333-99348340 chr2:99348330-99348340 chr2:99348329-99348343
22	MXI1	chr2:99347485-99348809	SK-N-SH	brain:	n/a	n/a
23	MAX	chr2:99347631-99349230	HepG2	liver:	n/a	n/a
24	HEY1	chr2:99346496-99349205	HepG2	liver:	n/a	chr2:99347342-99347357 chr2:99347044-99347059 chr2:99347015-99347030 chr2:99348124-99348139 chr2:99348047-99348062
25	RUNX3	chr2:99348058-99348513	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:99347674-99348539	GM12892	blood:	n/a	n/a
27	POLR2A	chr2:99348102-99348770	HepG2	liver:	n/a	n/a
28	MYC	chr2:99347715-99348411	NB4	blood:	n/a	n/a
29	MYBL2	chr2:99348012-99348850	HepG2	liver:	n/a	n/a
30	POLR2A	chr2:99347636-99348842	HUVEC	blood vessel:	n/a	n/a
31	CEBPB	chr2:99348249-99348809	HepG2	liver:	n/a	n/a
32	NR2F2	chr2:99347439-99349190	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:99347538-99348790	HUVEC	blood vessel:	n/a	n/a
34	EP300	chr2:99348080-99348854	HepG2	liver:	n/a	n/a
35	MAX	chr2:99347719-99348551	NB4	blood:	n/a	n/a
36	ARID3A	chr2:99348284-99349093	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:99347659-99348654	HL-60	blood:	n/a	n/a
38	POLR2A	chr2:99347399-99348755	HepG2	liver:	n/a	n/a
39	MTA3	chr2:99347973-99348575	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:99348080-99348648	GM12892	blood:	n/a	n/a
41	SIN3A	chr2:99347738-99348411	H1-hESC	embryonic stem cell:	n/a	chr2:99347912-99347925 chr2:99348095-99348108 chr2:99348082-99348095 chr2:99347988-99348001
42	POLR2A	chr2:99348038-99349260	HepG2	liver:	n/a	n/a
43	NFIC	chr2:99348124-99348805	HepG2	liver:	n/a	n/a
44	POLR2A	chr2:99347509-99348787	GM12892	blood:	n/a	n/a
45	TCF7L2	chr2:99348186-99348508	PANC-1	pancreas:	n/a	chr2:99348328-99348344 chr2:99348331-99348340 chr2:99348333-99348340 chr2:99348330-99348340 chr2:99348329-99348343
46	MAZ	chr2:99347653-99348397	GM12878	blood:	n/a	n/a
47	NR2F2	chr2:99348122-99348902	HepG2	liver:	n/a	n/a
48	POLR2A	chr2:99347686-99348362	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:99343338..99345259-chr2:99346373..99348700,3	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	chr2:99336480..99339286-chr2:99347871..99349769,2	MCF-7	breast:
6	chr2:99345368..99349321-chr2:99385005..99390572,6	MCF-7	breast:

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

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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:125 , 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	chr2:99345800-99348400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:99345800-99348400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:99345800-99348400	Active TSS	Ovary	ovary
13	chr2:99345800-99348400	Active TSS	Psoas Muscle	Psoas
14	chr2:99345800-99348400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr2:99345800-99348400	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr2:99345800-99348400	Active TSS	Small Intestine	intestine
17	chr2:99345800-99348600	Active TSS	Right Atrium	heart
18	chr2:99345800-99348800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr2:99345800-99348800	Active TSS	Fetal Intestine Small	intestine
20	chr2:99345800-99348800	Active TSS	Right Ventricle	heart
21	chr2:99345800-99349400	Active TSS	Pancreas	Pancrea
22	chr2:99346000-99348400	Active TSS	Brain Hippocampus Middle	brain
23	chr2:99346000-99348400	Active TSS	Brain Substantia Nigra	brain
24	chr2:99346000-99348600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr2:99346000-99348600	Bivalent/Poised TSS	HepG2	liver
26	chr2:99346200-99348400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr2:99346200-99348600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:99346200-99348600	Active TSS	Aorta	Aorta
29	chr2:99346200-99348800	Active TSS	Left Ventricle	heart
30	chr2:99346200-99348800	Active TSS	Lung	lung
31	chr2:99346200-99348800	Active TSS	Thymus	Thymus
32	chr2:99346400-99348400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:99346400-99348400	Active TSS	Brain Angular Gyrus	brain
34	chr2:99346400-99348600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr2:99346400-99348600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr2:99346600-99348400	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:99346600-99348400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:99346600-99348400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:99346600-99348400	Active TSS	Esophagus	oesophagus
40	chr2:99346600-99348400	Active TSS	Gastric	stomach
41	chr2:99346600-99348400	Bivalent/Poised TSS	HSMM	muscle
42	chr2:99346600-99348600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:99346800-99348400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr2:99346800-99348600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
45	chr2:99346800-99348600	Active TSS	Colon Smooth Muscle	Colon
46	chr2:99347000-99348400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:99347000-99348400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:99347000-99348600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:99347200-99348400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:99347800-99348400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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