Variant report

Variant	rs2745596
Chromosome Location	chr6:1606031-1606032
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:1605336-1607113	H1-neurons	neurons:	n/a	n/a
2	CTBP2	chr6:1605896-1607554	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr6:1606000-1606150	HepG2	liver:	n/a	chr6:1606083-1606092
4	SUZ12	chr6:1604280-1606844	NT2-D1	testis:	n/a	n/a
5	SUZ12	chr6:1604488-1607142	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:1604616-1606837	H1-neurons	neurons:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:1606028-1606078	ovcar-3	ovarian:	n/a
2	chr6:1606028-1606078	AG09319	gingival:	n/a
3	chr6:1606028-1606078	HNPCEpiC	eye:	n/a
4	chr6:1606028-1606078	K562	blood:	n/a
5	chr6:1606028-1606078	U87	brain:	n/a
6	chr6:1606028-1606078	HPAEpiC	pulmonary alveolar:	n/a
7	chr6:1606028-1606078	ProgFib	skin:	n/a
8	chr6:1606028-1606078	HRE	kidney:	n/a
9	chr6:1606028-1606078	PANC-1	pancreas:	n/a
10	chr6:1606028-1606078	T-47D	breast:	n/a
11	chr6:1606028-1606078	SAEC	small airway:	n/a
12	chr6:1606028-1606078	Caco-2	colon:	n/a
13	chr6:1606028-1606078	GM19239	blood:	n/a
14	chr6:1606028-1606078	GM12891	blood:	n/a
15	chr6:1606028-1606078	AG09309	skin:	n/a
16	chr6:1606028-1606078	LNCaP	prostate:	n/a
17	chr6:1606028-1606078	ECC-1	luminal epithelium:	n/a
18	chr6:1606028-1606078	Jurkat	blood:	n/a
19	chr6:1606028-1606078	HEEpiC	esophagus:	n/a
20	chr6:1606028-1606078	A549	lung:	n/a
21	chr6:1606028-1606078	BJ	skin:	n/a
22	chr6:1606028-1606078	HAEpiC	amniotic membrane:	n/a
23	chr6:1606028-1606078	RPTEC	kidney:	n/a
24	chr6:1606028-1606078	GM12878	blood:	n/a
25	chr6:1606028-1606078	HMEC	breast:	n/a
26	chr6:1606028-1606078	SK-N-MC	brain:	n/a
27	chr6:1606028-1606078	HUVEC	blood vessel:	n/a
28	chr6:1606028-1606078	NHBE	bronchial:	n/a
29	chr6:1606028-1606078	MCF-7	breast:	n/a
30	chr6:1606028-1606078	BE2_C	brain:	n/a
31	chr6:1606028-1606078	GM06990	blood:	n/a
32	chr6:1606028-1606078	MCF10A-Er-Src	breast:	n/a
33	chr6:1606028-1606078	Hela-S3	cervix:	n/a
34	chr6:1606028-1606078	NH-A	brain:	n/a
35	chr6:1606028-1606078	Hepatocyte	liver:	n/a
36	chr6:1606028-1606078	CMK	blood:	n/a
37	chr6:1606028-1606078	AG04449	skin:	fetal
38	chr6:1606028-1606078	NT2-D1	testis:	n/a
39	chr6:1606028-1606078	HepG2	liver:	n/a
40	chr6:1606028-1606078	HIPEpiC	eye:	n/a
41	chr6:1606028-1606078	HCM	heart:	n/a
42	chr6:1606028-1606078	PFSK-1	brain:	n/a
43	chr6:1606028-1606078	AG10803	skin:	n/a
44	chr6:1606028-1606078	HCF	heart:	n/a
45	chr6:1606028-1606078	GM12892	blood:	n/a
46	chr6:1606028-1606078	H1-hESC	embryonic stem cell:	embryo
47	chr6:1606028-1606078	AoSMC	blood vessel:	n/a
48	chr6:1606028-1606078	SK-N-SH	brain:	n/a
49	chr6:1606028-1606078	HL-60	blood:	n/a
50	chr6:1606028-1606078	SK-N-SH_RA	brain:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1605093..1609098-chr6:1671097..1673871,3	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXC1-1	chr6:1605724-1606034	XLOC_005125
2	lnc-GMDS-6	chr6:1605756-1606556	NONHSAT106519
3	lnc-GMDS-6	chr6:1603265-1608466	NONHSAT106529
4	lnc-GMDS-6	chr6:1605088-1607351	NONHSAT106531

No data

Variant related genes	Relation type
FOXC1	TF binding region
FOXC1	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2745595	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2745599	0.84[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv917248	chr6:1365437-1627813	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1034039	chr6:1427061-1691837	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv538088	chr6:1427061-1691837	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv1027393	chr6:1446300-1692019	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv538089	chr6:1446300-1692019	Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv1016859	chr6:1460020-1645819	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv883376	chr6:1535043-1635082	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv1016594	chr6:1590030-1702529	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	nsv823394	chr6:1590091-1629146	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
15	nsv883378	chr6:1593851-1623990	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	nsv883379	chr6:1593851-1628902	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
17	nsv823395	chr6:1595031-1629521	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
18	nsv883380	chr6:1595216-1621404	Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
19	nsv883381	chr6:1595216-1628902	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
20	nsv823396	chr6:1597359-1629106	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
21	nsv883382	chr6:1598942-1620037	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
22	esv3439668	chr6:1603778-1606326	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv823397	chr6:1603867-1622264	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
24	nsv530888	chr6:1605768-1739933	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2745596	FAM50B	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1604200-1610800	Active TSS	Aorta	Aorta
2	chr6:1604400-1606200	Bivalent Enhancer	Fetal Stomach	stomach
3	chr6:1604400-1606400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:1604400-1610800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:1604800-1609600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
6	chr6:1605000-1606200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:1605000-1606400	Bivalent Enhancer	Brain Germinal Matrix	brain
8	chr6:1605000-1606400	Bivalent Enhancer	Stomach Mucosa	stomach
9	chr6:1605000-1607400	Bivalent Enhancer	GM12878-XiMat	blood
10	chr6:1605000-1607600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
11	chr6:1605000-1609400	Bivalent Enhancer	Fetal Thymus	thymus
12	chr6:1605000-1610800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr6:1605200-1606200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:1605200-1606200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
15	chr6:1605200-1606200	Bivalent Enhancer	Liver	Liver
16	chr6:1605200-1606200	Bivalent Enhancer	Fetal Intestine Large	intestine
17	chr6:1605200-1606200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr6:1605200-1606400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
19	chr6:1605200-1608800	Weak transcription	Hela-S3	cervix
20	chr6:1605200-1609600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr6:1605400-1606400	Bivalent/Poised TSS	Osteobl	bone
22	chr6:1605400-1607000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:1605400-1607000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
24	chr6:1605400-1607800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:1605400-1608000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
26	chr6:1605400-1609000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:1605400-1609000	Weak transcription	HMEC	breast
28	chr6:1605400-1609400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
29	chr6:1605400-1609400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:1605400-1609400	Bivalent Enhancer	Fetal Muscle Leg	muscle
31	chr6:1605600-1606800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
32	chr6:1605600-1607000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:1605600-1607200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
34	chr6:1605600-1607800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:1605600-1607800	Weak transcription	Gastric	stomach
36	chr6:1605600-1609000	Enhancers	Pancreas	Pancrea
37	chr6:1605600-1609000	Weak transcription	Right Atrium	heart
38	chr6:1605600-1609400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
39	chr6:1605600-1620800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:1605800-1606200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr6:1605800-1606200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
42	chr6:1605800-1606200	Bivalent Enhancer	Primary B cells from cord blood	blood
43	chr6:1605800-1606200	Weak transcription	Spleen	Spleen
44	chr6:1605800-1606400	Bivalent Enhancer	Fetal Heart	heart
45	chr6:1605800-1606600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:1605800-1606600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:1605800-1607200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
48	chr6:1605800-1607600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
49	chr6:1605800-1607600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:1605800-1608000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood

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