Variant report

Variant	rs2788996
Chromosome Location	chr6:118228527-118228528
allele	G/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	REST	chr6:118227755-118228545	HL-60	blood:	n/a	chr6:118228087-118228100 chr6:118228087-118228096 chr6:118228100-118228114
2	ZBTB7A	chr6:118228016-118228550	ECC-1	luminal epithelium:	n/a	chr6:118228288-118228297
3	TAF1	chr6:118228363-118229916	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr6:118228068-118229176	HepG2	liver:	n/a	chr6:118228320-118228330
5	CTCF	chr6:118228118-118228568	GM12891	blood:	n/a	chr6:118228288-118228304
6	CTCF	chr6:118228420-118228570	SK-N-SH_RA	brain:	n/a	n/a
7	E2F6	chr6:118228403-118229958	H1-hESC	embryonic stem cell:	n/a	chr6:118228467-118228477 chr6:118228719-118228729 chr6:118228565-118228574 chr6:118229452-118229461
8	TAF1	chr6:118228226-118228677	H1-neurons	neurons:	n/a	n/a
9	MAZ	chr6:118227924-118228570	HepG2	liver:	n/a	chr6:118228320-118228330
10	MAX	chr6:118228424-118229829	ECC-1	luminal epithelium:	n/a	chr6:118229743-118229753
11	MAX	chr6:118228422-118228622	HepG2	liver:	n/a	n/a
12	CTCF	chr6:118228091-118228577	K562	blood:	n/a	chr6:118228288-118228304
13	EP300	chr6:118227949-118228601	SK-N-SH	brain:	n/a	chr6:118228560-118228576 chr6:118228088-118228104
14	CTCF	chr6:118227742-118228634	SK-N-SH	brain:	n/a	chr6:118228288-118228304
15	REST	chr6:118227712-118229252	ECC-1	luminal epithelium:	n/a	chr6:118228087-118228100 chr6:118228087-118228096 chr6:118228100-118228114
16	EP300	chr6:118227918-118228650	H1-hESC	embryonic stem cell:	n/a	chr6:118228560-118228576 chr6:118228088-118228104
17	REST	chr6:118227770-118228623	HepG2	liver:	n/a	chr6:118228087-118228100 chr6:118228087-118228096 chr6:118228100-118228114
18	CTCF	chr6:118228440-118228590	GM12871	blood:	n/a	n/a
19	POLR2A	chr6:118228098-118229882	H1-neurons	neurons:	n/a	n/a
20	MAX	chr6:118227943-118229895	H1-hESC	embryonic stem cell:	n/a	chr6:118228320-118228330 chr6:118229743-118229753
21	MAX	chr6:118227892-118229881	H1-hESC	embryonic stem cell:	n/a	chr6:118228320-118228330 chr6:118229743-118229753
22	POLR2A	chr6:118227774-118229983	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr6:118228420-118228570	GM12864	blood:	n/a	n/a
24	TBP	chr6:118228027-118228878	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr6:118228400-118228550	HRPEpiC	eye:	n/a	n/a
26	POLR2A	chr6:118227938-118229722	HEK293	kidney:	n/a	n/a
27	CHD1	chr6:118228478-118228536	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr6:118228355-118228597	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr6:118228420-118228570	GM12869	blood:	n/a	n/a
30	CTBP2	chr6:118227970-118229940	H1-hESC	embryonic stem cell:	n/a	n/a
31	BACH1	chr6:118228015-118228606	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr6:118228067-118229111	H1-neurons	neurons:	n/a	n/a
33	TAF7	chr6:118227976-118228600	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr6:118228473-118229224	HepG2	liver:	n/a	n/a
35	SIN3A	chr6:118227873-118230094	H1-hESC	embryonic stem cell:	n/a	chr6:118228087-118228100 chr6:118228711-118228722
36	CTCF	chr6:118228440-118228590	GM12866	blood:	n/a	n/a
37	EP300	chr6:118227944-118228793	ECC-1	luminal epithelium:	n/a	chr6:118228720-118228729 chr6:118228560-118228576 chr6:118228696-118228709 chr6:118228088-118228104
38	POLR2A	chr6:118228351-118228616	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr6:118227969-118228593	A549	lung:	n/a	chr6:118228288-118228304
40	POLR2A	chr6:118228129-118229717	H1-hESC	embryonic stem cell:	n/a	n/a
41	REST	chr6:118227381-118228844	HL-60	blood:	n/a	chr6:118228087-118228100 chr6:118227707-118227715 chr6:118228087-118228096 chr6:118228100-118228114
42	REST	chr6:118227649-118230270	H1-neurons	neurons:	n/a	chr6:118228087-118228100 chr6:118227707-118227715 chr6:118228087-118228096 chr6:118228100-118228114

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:118228493-118228543	Jurkat	blood:	n/a
2	chr6:118228508-118228558	HPAEpiC	pulmonary alveolar:	n/a
3	chr6:118228508-118228558	SK-N-SH_RA	brain:	n/a
4	chr6:118228514-118228564	U87	brain:	n/a
5	chr6:118228493-118228543	HEK293	kidney:	embryo
6	chr6:118228493-118228543	GM06990	blood:	n/a
7	chr6:118228498-118228548	AG04449	skin:	fetal
8	chr6:118228514-118228564	NH-A	brain:	n/a
9	chr6:118228514-118228564	GM12892	blood:	n/a
10	chr6:118228493-118228543	NHBE	bronchial:	n/a
11	chr6:118228514-118228564	GM12878	blood:	n/a
12	chr6:118228493-118228543	ECC-1	luminal epithelium:	n/a
13	chr6:118228498-118228548	HRCEpiC	kidney:	n/a
14	chr6:118228508-118228558	K562	blood:	n/a
15	chr6:118228493-118228543	PANC-1	pancreas:	n/a
16	chr6:118228514-118228564	Jurkat	blood:	n/a
17	chr6:118228498-118228548	RPTEC	kidney:	n/a
18	chr6:118228498-118228548	HCT-116	colon:	n/a
19	chr6:118228498-118228548	T-47D	breast:	n/a
20	chr6:118228493-118228543	PrEC	prostate:	n/a
21	chr6:118228498-118228548	A549	lung:	n/a
22	chr6:118228508-118228558	HepG2	liver:	n/a
23	chr6:118228498-118228548	U87	brain:	n/a
24	chr6:118228493-118228543	MCF10A-Er-Src	breast:	n/a
25	chr6:118228514-118228564	HPAEpiC	pulmonary alveolar:	n/a
26	chr6:118228493-118228543	HMEC	breast:	n/a
27	chr6:118228493-118228543	HNPCEpiC	eye:	n/a
28	chr6:118228514-118228564	AoSMC	blood vessel:	n/a
29	chr6:118228498-118228548	HPAEpiC	pulmonary alveolar:	n/a
30	chr6:118228508-118228558	GM12892	blood:	n/a
31	chr6:118228498-118228548	HCF	heart:	n/a
32	chr6:118228493-118228543	PFSK-1	brain:	n/a
33	chr6:118228493-118228543	AG04450	lung:	fetal
34	chr6:118228493-118228543	Hepatocyte	liver:	n/a
35	chr6:118228514-118228564	CMK	blood:	n/a
36	chr6:118228498-118228548	AG04450	lung:	fetal
37	chr6:118228508-118228558	BJ	skin:	n/a
38	chr6:118228493-118228543	GM12892	blood:	n/a
39	chr6:118228498-118228548	GM19239	blood:	n/a
40	chr6:118228514-118228564	H1-hESC	embryonic stem cell:	embryo
41	chr6:118228493-118228543	HIPEpiC	eye:	n/a
42	chr6:118228508-118228558	A549	lung:	n/a
43	chr6:118228493-118228543	HCM	heart:	n/a
44	chr6:118228498-118228548	HRPEpiC	eye:	n/a
45	chr6:118228493-118228543	MCF-7	breast:	n/a
46	chr6:118228493-118228543	HUVEC	blood vessel:	n/a
47	chr6:118228508-118228558	GM06990	blood:	n/a
48	chr6:118228498-118228548	HNPCEpiC	eye:	n/a
49	chr6:118228498-118228548	K562	blood:	n/a
50	chr6:118228493-118228543	GM12891	blood:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:118161401..118162100-chr6:118227994..118228639,2	MCF-7	breast:

Variant related genes	Relation type
SLC35F1	TF binding region
SLC35F1	CpG island

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13192257	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1338977	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs17079565	0.87[CHB][hapmap]
rs17079574	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2355790	0.87[CHB][hapmap]

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	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	esv3414441	chr6:118227509-118229957	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv522455	chr6:118228527-118240685	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2788996	CAB39L	trans	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118227400-118230200	Active TSS	Brain Angular Gyrus	brain
2	chr6:118227400-118230400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:118227600-118228800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:118227600-118228800	Active TSS	Stomach Smooth Muscle	stomach
5	chr6:118227600-118229000	Bivalent Enhancer	Liver	Liver
6	chr6:118227600-118229000	Active TSS	Brain Germinal Matrix	brain
7	chr6:118227600-118229400	Active TSS	Fetal Brain Female	brain
8	chr6:118227600-118229600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
9	chr6:118227600-118230000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr6:118227600-118230000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:118227800-118228600	Active TSS	Psoas Muscle	Psoas
12	chr6:118227800-118228600	Bivalent/Poised TSS	Right Ventricle	heart
13	chr6:118227800-118228600	Bivalent/Poised TSS	HUVEC	blood vessel
14	chr6:118227800-118228800	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:118227800-118228800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:118227800-118228800	Active TSS	Right Atrium	heart
17	chr6:118227800-118229000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:118227800-118229200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr6:118227800-118229200	Active TSS	Left Ventricle	heart
20	chr6:118227800-118229400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
21	chr6:118227800-118229400	Active TSS	Rectal Smooth Muscle	rectum
22	chr6:118227800-118229600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:118227800-118229600	Bivalent/Poised TSS	A549	lung
24	chr6:118227800-118229800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:118227800-118229800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:118227800-118230000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:118227800-118230200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:118227800-118230400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:118227800-118230400	Active TSS	Brain Cingulate Gyrus	brain
30	chr6:118227800-118230400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
31	chr6:118228000-118228600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:118228000-118228600	Active TSS	Colonic Mucosa	Colon
33	chr6:118228000-118228600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
34	chr6:118228000-118228600	Active TSS	Fetal Lung	lung
35	chr6:118228000-118228800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:118228000-118228800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:118228000-118229000	Bivalent/Poised TSS	HSMMtube	muscle
38	chr6:118228000-118229000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
39	chr6:118228000-118229200	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr6:118228000-118229200	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr6:118228000-118229200	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
42	chr6:118228000-118229200	Active TSS	Pancreas	Pancrea
43	chr6:118228000-118229200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
44	chr6:118228000-118229200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
45	chr6:118228000-118229200	Active TSS	HSMM	muscle
46	chr6:118228000-118229200	Active TSS	NH-A	brain
47	chr6:118228000-118229200	Bivalent/Poised TSS	NHEK	skin
48	chr6:118228000-118229400	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr6:118228000-118229400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:118228000-118229400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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