Variant report

Variant	rs6438648
Chromosome Location	chr3:121379169-121379170
allele	A/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	chr3:121379160-121380045	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr3:121378460-121380063	GM12891	blood:	n/a	n/a
3	POLR2A	chr3:121378892-121380528	Raji	blood:	n/a	n/a
4	POLR2A	chr3:121378769-121380414	GM12891	blood:	n/a	n/a
5	ZNF143	chr3:121379132-121379917	GM12878	blood:	n/a	n/a
6	BCLAF1	chr3:121378976-121380116	GM12878	blood:	n/a	n/a
7	STAT1	chr3:121378909-121379831	GM12878	blood:	n/a	n/a
8	CHD2	chr3:121379090-121379951	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:121378647-121380088	GM12892	blood:	n/a	n/a
10	POU2F2	chr3:121379068-121379953	GM12891	blood:	n/a	n/a
11	MAFK	chr3:121378918-121379232	HepG2	liver:	n/a	chr3:121379065-121379076 chr3:121379065-121379076 chr3:121379063-121379077 chr3:121379060-121379075
12	ELF1	chr3:121378986-121380031	GM12878	blood:	n/a	chr3:121379820-121379833
13	STAT5A	chr3:121378879-121380125	GM12878	blood:	n/a	n/a
14	MAX	chr3:121379137-121380184	GM12878	blood:	n/a	n/a
15	PML	chr3:121378919-121379962	GM12878	blood:	n/a	chr3:121379202-121379210
16	MAX	chr3:121379146-121380085	NB4	blood:	n/a	n/a
17	NFATC1	chr3:121378755-121380352	GM12878	blood:	n/a	chr3:121379083-121379097
18	WRNIP1	chr3:121378160-121380048	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:121378663-121379973	GM12878	blood:	n/a	n/a
20	CREB1	chr3:121379046-121380091	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:121378409-121380015	GM12891	blood:	n/a	n/a
22	POLR2A	chr3:121378844-121382265	K562	blood:	n/a	n/a
23	BCLAF1	chr3:121379038-121380039	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:121378678-121379946	GM15510	blood:	n/a	n/a
25	MAFK	chr3:121378938-121379177	HepG2	liver:	n/a	chr3:121379065-121379076 chr3:121379065-121379076 chr3:121379063-121379077 chr3:121379060-121379075
26	POLR2A	chr3:121378045-121380888	GM12878	blood:	n/a	n/a
27	NFATC1	chr3:121378657-121380660	GM12878	blood:	n/a	chr3:121379083-121379097
28	POU2F2	chr3:121379124-121379873	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:121379066-121379869	GM12878	blood:	n/a	n/a
30	YY1	chr3:121379059-121379863	GM12878	blood:	n/a	n/a
31	RCOR1	chr3:121379036-121380008	GM12878	blood:	n/a	n/a
32	NFIC	chr3:121379081-121380221	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:121378965-121380251	GM12878	blood:	n/a	n/a
34	MYC	chr3:121379111-121380516	NB4	blood:	n/a	n/a
35	CHD1	chr3:121378843-121380022	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:121379034-121381303	HepG2	liver:	n/a	n/a
37	POLR2A	chr3:121376697-121380815	GM12891	blood:	n/a	n/a
38	RELA	chr3:121379030-121380048	GM12891	blood:	n/a	n/a
39	MTA3	chr3:121378972-121380460	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:121378856-121380005	GM18526	blood:	n/a	n/a
41	POLR2A	chr3:121379047-121380257	HUVEC	blood vessel:	n/a	n/a
42	RELA	chr3:121378565-121380440	GM18505	blood:	n/a	n/a
43	RUNX3	chr3:121379066-121379985	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:121378837-121381282	Hela-S3	cervix:	n/a	n/a
45	PML	chr3:121378506-121380475	GM12878	blood:	n/a	chr3:121379202-121379210
46	POLR2A	chr3:121377924-121380942	GM12878	blood:	n/a	n/a
47	RELA	chr3:121379033-121379957	GM18951	blood:	n/a	n/a
48	STAT3	chr3:121378863-121380149	GM12878	blood:	n/a	chr3:121380118-121380126
49	CEBPB	chr3:121378977-121380300	GM12878	blood:	n/a	chr3:121379054-121379065
50	POLR2A	chr3:121377943-121380122	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
RNU4-62P	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs34740909	1.00[EUR][1000 genomes]
rs61750878	1.00[EUR][1000 genomes]
rs6789527	1.00[EUR][1000 genomes]
rs7627703	1.00[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	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS 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	18 gene(s)	inside rSNPs	diseases
5	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121348000-121381800	Weak transcription	Aorta	Aorta
2	chr3:121351000-121382800	Weak transcription	Small Intestine	intestine
3	chr3:121351400-121381400	Weak transcription	Gastric	stomach
4	chr3:121354000-121381000	Weak transcription	Fetal Intestine Small	intestine
5	chr3:121356800-121379200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:121362200-121379400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:121362600-121379600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:121367400-121381800	Weak transcription	Pancreas	Pancrea
9	chr3:121368800-121380000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:121370600-121379400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:121370600-121381600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:121371000-121383600	Weak transcription	Hela-S3	cervix
13	chr3:121373000-121380400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:121374000-121379600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:121374800-121380000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:121376400-121382200	Weak transcription	A549	lung
17	chr3:121376400-121383000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:121377000-121383600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:121377200-121379200	Weak transcription	Esophagus	oesophagus
20	chr3:121377400-121379400	Enhancers	Lung	lung
21	chr3:121377400-121380800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr3:121377600-121379200	Enhancers	Left Ventricle	heart
23	chr3:121377600-121379200	Enhancers	Spleen	Spleen
24	chr3:121377600-121379400	Transcr. at gene 5' and 3'	Dnd41	blood
25	chr3:121377600-121379600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:121377800-121379400	Weak transcription	Fetal Intestine Large	intestine
27	chr3:121377800-121379400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr3:121377800-121381600	Weak transcription	Fetal Brain Female	brain
29	chr3:121378000-121379200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:121378000-121379200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr3:121378000-121379200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr3:121378000-121379200	Enhancers	Right Ventricle	heart
33	chr3:121378000-121380000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr3:121378000-121380400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:121378000-121388400	Strong transcription	Fetal Stomach	stomach
36	chr3:121378200-121379200	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
37	chr3:121378200-121379200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr3:121378200-121379200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr3:121378200-121379400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:121378200-121379800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr3:121378200-121379800	Active TSS	Brain Anterior Caudate	brain
42	chr3:121378200-121379800	Active TSS	Brain Hippocampus Middle	brain
43	chr3:121378200-121379800	Active TSS	Colonic Mucosa	Colon
44	chr3:121378200-121379800	Active TSS	Rectal Smooth Muscle	rectum
45	chr3:121378200-121380000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr3:121378200-121380000	Weak transcription	NHEK	skin
47	chr3:121378200-121380200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:121378200-121381600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:121378400-121379200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:121378400-121379400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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