Variant report

Variant	rs2493331
Chromosome Location	chr6:24911471-24911472
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	JUND	chr6:24911132-24911629	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZBTB7A	chr6:24911148-24911628	ECC-1	luminal epithelium:	n/a	n/a
3	EGR1	chr6:24911164-24911472	GM12878	blood:	n/a	n/a
4	ZNF143	chr6:24911421-24911606	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:24911079-24911552	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUND	chr6:24911378-24911569	H1-hESC	embryonic stem cell:	n/a	n/a
7	MXI1	chr6:24910900-24911644	H1-hESC	embryonic stem cell:	n/a	n/a
8	PAX5	chr6:24911321-24911821	GM12878	blood:	n/a	n/a
9	PAX5	chr6:24911070-24911677	GM12892	blood:	n/a	n/a
10	TAF1	chr6:24910614-24911770	H1-neurons	neurons:	n/a	n/a
11	CHD1	chr6:24911408-24911605	GM12878	blood:	n/a	n/a
12	REST	chr6:24909853-24911705	H1-neurons	neurons:	n/a	chr6:24910158-24910168 chr6:24910153-24910166 chr6:24910150-24910170
13	POLR2A	chr6:24910958-24912088	GM12878	blood:	n/a	n/a
14	MAX	chr6:24911084-24911615	SK-N-SH	brain:	n/a	n/a
15	HDAC2	chr6:24911396-24911580	H1-hESC	embryonic stem cell:	n/a	n/a
16	PAX5	chr6:24911248-24911688	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:24909844-24911809	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr6:24911041-24911547	GM12878	blood:	n/a	n/a
19	CHD2	chr6:24910173-24911550	GM12878	blood:	n/a	chr6:24910399-24910409
20	CTCF	chr6:24911420-24911570	AG04449	skin:	n/a	n/a
21	MAZ	chr6:24910272-24911710	GM12878	blood:	n/a	n/a
22	CTBP2	chr6:24910045-24911760	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr6:24909193-24911613	GM12891	blood:	n/a	n/a
24	TCF12	chr6:24911321-24911564	GM12878	blood:	n/a	n/a
25	TCF12	chr6:24911235-24911683	ECC-1	luminal epithelium:	n/a	n/a
26	PAX5	chr6:24911319-24911553	GM12878	blood:	n/a	n/a
27	PAX5	chr6:24910499-24911771	GM12878	blood:	n/a	n/a
28	TBP	chr6:24911093-24911625	H1-hESC	embryonic stem cell:	n/a	n/a
29	SIN3A	chr6:24910027-24912091	H1-hESC	embryonic stem cell:	n/a	chr6:24911423-24911431
30	MAX	chr6:24911068-24911656	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAZ	chr6:24910821-24912173	IMR90	lung:	n/a	n/a
32	TEAD4	chr6:24911257-24911517	H1-hESC	embryonic stem cell:	n/a	n/a
33	RAD21	chr6:24911047-24911636	H1-hESC	embryonic stem cell:	n/a	chr6:24911452-24911465 chr6:24911593-24911605
34	POLR2A	chr6:24910597-24911651	GM19193	blood:	n/a	n/a
35	POLR2A	chr6:24911436-24911501	Gliobla	brain:	n/a	n/a
36	CHD2	chr6:24911467-24911655	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr6:24911361-24911560	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:24910127-24911819	GM18505	blood:	n/a	n/a
39	POLR2A	chr6:24910817-24911534	GM12878	blood:	n/a	n/a
40	SIN3AK20	chr6:24911280-24911650	H1-hESC	embryonic stem cell:	n/a	n/a
41	ELF1	chr6:24910387-24911674	GM12878	blood:	n/a	chr6:24910709-24910721
42	CHD1	chr6:24911435-24911620	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr6:24911409-24911523	MCF-7	breast:	n/a	n/a
44	CREB1	chr6:24911147-24911637	H1-hESC	embryonic stem cell:	n/a	n/a
45	TCF12	chr6:24911274-24911557	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:24911036-24911692	ProgFib	skin:	n/a	n/a
47	POLR2A	chr6:24909904-24911933	H1-neurons	neurons:	n/a	n/a
48	MXI1	chr6:24910180-24911987	SK-N-SH	brain:	n/a	chr6:24910490-24910499
49	MAX	chr6:24910824-24911799	GM12878	blood:	n/a	n/a
50	MXI1	chr6:24910840-24911588	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
FAM65B	TF binding region

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2064524	0.86[ASN][1000 genomes]
rs2207399	0.93[ASN][1000 genomes]
rs2747674	0.91[ASN][1000 genomes]
rs2747675	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2747676	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817722	0.84[EUR][1000 genomes]
rs2817727	0.91[ASN][1000 genomes]
rs2817729	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2817731	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817733	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs932494	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24908000-24912200	Active TSS	HSMMtube	muscle
2	chr6:24908200-24912600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:24908600-24913200	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
4	chr6:24908600-24913600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
5	chr6:24908800-24911600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr6:24909000-24911800	Active TSS	Brain Angular Gyrus	brain
7	chr6:24909000-24913400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
8	chr6:24909200-24911800	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr6:24909200-24912200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:24909400-24912000	Active TSS	Brain Cingulate Gyrus	brain
11	chr6:24909400-24912000	Active TSS	Rectal Smooth Muscle	rectum
12	chr6:24909600-24911800	Active TSS	Brain Substantia Nigra	brain
13	chr6:24909600-24912400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:24909600-24912400	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:24909600-24913600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
16	chr6:24909600-24913600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
17	chr6:24909600-24914200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
18	chr6:24909600-24918000	Weak transcription	Dnd41	blood
19	chr6:24909800-24911600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:24909800-24911600	Active TSS	Brain Anterior Caudate	brain
21	chr6:24909800-24911600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
22	chr6:24909800-24911600	Active TSS	Left Ventricle	heart
23	chr6:24909800-24911800	Active TSS	Colon Smooth Muscle	Colon
24	chr6:24909800-24911800	Active TSS	HSMM	muscle
25	chr6:24909800-24912000	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr6:24909800-24912600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:24910000-24911600	Bivalent/Poised TSS	Osteobl	bone
28	chr6:24910000-24911800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr6:24910000-24911800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr6:24910000-24912000	Active TSS	Ovary	ovary
31	chr6:24910200-24911800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
32	chr6:24910200-24911800	Flanking Active TSS	Liver	Liver
33	chr6:24910200-24911800	Active TSS	Fetal Kidney	kidney
34	chr6:24910200-24912000	Bivalent/Poised TSS	NHLF	lung
35	chr6:24910200-24912200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:24910400-24911600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
37	chr6:24910400-24911800	Active TSS	Fetal Heart	heart
38	chr6:24910400-24912000	Active TSS	H9 Cell Line	embryonic stem cell
39	chr6:24910400-24912000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:24910400-24912000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr6:24910400-24912000	Active TSS	NHDF-Ad	bronchial
42	chr6:24910400-24912200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:24910400-24912400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr6:24910400-24913000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:24910600-24911600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
46	chr6:24910600-24911600	Active TSS	Gastric	stomach
47	chr6:24910600-24911600	Active TSS	Psoas Muscle	Psoas
48	chr6:24910600-24911800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:24910600-24911800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr6:24910600-24911800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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