Variant report

Variant	rs3756821
Chromosome Location	chr6:24646821-24646822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TFAP2C	chr6:24645783-24647140	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr6:24645895-24647439	IMR90	lung:	n/a	chr6:24646440-24646455 chr6:24646438-24646453
3	GATA3	chr6:24646750-24647147	MCF-7	breast:	n/a	n/a
4	TFAP2A	chr6:24645759-24647092	Hela-S3	cervix:	n/a	n/a
5	BRCA1	chr6:24646478-24647068	Hela-S3	cervix:	n/a	n/a
6	RFX5	chr6:24645329-24647270	Hela-S3	cervix:	n/a	chr6:24646439-24646454 chr6:24646439-24646454 chr6:24646438-24646455 chr6:24646439-24646454
7	RCOR1	chr6:24646646-24646827	HepG2	liver:	n/a	n/a
8	SMARCC1	chr6:24645792-24646882	Hela-S3	cervix:	n/a	n/a
9	RCOR1	chr6:24645755-24646929	IMR90	lung:	n/a	n/a
10	MXI1	chr6:24645691-24646852	Hela-S3	cervix:	n/a	chr6:24646440-24646455 chr6:24646438-24646453
11	POLR2A	chr6:24645888-24646903	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr6:24645671-24647135	SK-N-SH	brain:	n/a	chr6:24646440-24646455 chr6:24646438-24646453
13	RCOR1	chr6:24645735-24646852	K562	blood:	n/a	n/a
14	HMGN3	chr6:24645871-24646839	K562	blood:	n/a	n/a
15	MAZ	chr6:24645757-24647142	Hela-S3	cervix:	n/a	n/a
16	SMARCB1	chr6:24645809-24646846	Hela-S3	cervix:	n/a	n/a
17	MAFK	chr6:24645724-24646873	Hela-S3	cervix:	n/a	n/a
18	RCOR1	chr6:24645653-24647241	Hela-S3	cervix:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:24646782-24646832	HCT-116	colon:	n/a
2	chr6:24646782-24646832	AG04449	skin:	fetal
3	chr6:24646782-24646832	PrEC	prostate:	n/a
4	chr6:24646782-24646832	SK-N-MC	brain:	n/a
5	chr6:24646782-24646832	NB4	blood:	n/a
6	chr6:24646782-24646832	HepG2	liver:	n/a
7	chr6:24646782-24646832	HAEpiC	amniotic membrane:	n/a
8	chr6:24646782-24646832	HCF	heart:	n/a
9	chr6:24646782-24646832	NH-A	brain:	n/a
10	chr6:24646782-24646832	LNCaP	prostate:	n/a
11	chr6:24646782-24646832	GM12892	blood:	n/a
12	chr6:24646782-24646832	GM12878	blood:	n/a
13	chr6:24646782-24646832	HCPEpiC	choroid plexus:	n/a
14	chr6:24646782-24646832	CMK	blood:	n/a
15	chr6:24646782-24646832	PANC-1	pancreas:	n/a
16	chr6:24646782-24646832	GM19239	blood:	n/a
17	chr6:24646782-24646832	HEK293	kidney:	embryo
18	chr6:24646782-24646832	HCM	heart:	n/a
19	chr6:24646782-24646832	HNPCEpiC	eye:	n/a
20	chr6:24646782-24646832	U87	brain:	n/a
21	chr6:24646782-24646832	SKMC	muscle:	n/a
22	chr6:24646782-24646832	BJ	skin:	n/a
23	chr6:24646782-24646832	GM06990	blood:	n/a
24	chr6:24646782-24646832	SK-N-SH	brain:	n/a
25	chr6:24646782-24646832	H1-hESC	embryonic stem cell:	embryo
26	chr6:24646782-24646832	MCF-7	breast:	n/a
27	chr6:24646782-24646832	HRE	kidney:	n/a
28	chr6:24646782-24646832	HRPEpiC	eye:	n/a
29	chr6:24646782-24646832	PFSK-1	brain:	n/a
30	chr6:24646782-24646832	Hela-S3	cervix:	n/a
31	chr6:24646782-24646832	Jurkat	blood:	n/a
32	chr6:24646782-24646832	AoSMC	blood vessel:	n/a
33	chr6:24646782-24646832	HUVEC	blood vessel:	n/a
34	chr6:24646782-24646832	MCF10A-Er-Src	breast:	n/a
35	chr6:24646782-24646832	NHBE	bronchial:	n/a
36	chr6:24646782-24646832	A549	lung:	n/a
37	chr6:24646782-24646832	NHDF-neo	bronchial:	n/a
38	chr6:24646782-24646832	AG04450	lung:	fetal
39	chr6:24646782-24646832	Caco-2	colon:	n/a
40	chr6:24646782-24646832	HMEC	breast:	n/a
41	chr6:24646782-24646832	HRCEpiC	kidney:	n/a
42	chr6:24646782-24646832	Hepatocyte	liver:	n/a
43	chr6:24646782-24646832	HEEpiC	esophagus:	n/a
44	chr6:24646782-24646832	ProgFib	skin:	n/a
45	chr6:24646782-24646832	AG09309	skin:	n/a
46	chr6:24646782-24646832	IMR90	lung:	fetal
47	chr6:24646782-24646832	RPTEC	kidney:	n/a
48	chr6:24646782-24646832	HPAEpiC	pulmonary alveolar:	n/a
49	chr6:24646782-24646832	BE2_C	brain:	n/a
50	chr6:24646782-24646832	K562	blood:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24644992..24647314-chr6:24719656..24721157,2	MCF-7	breast:
2	chr6:24645396..24648521-chr6:24658092..24661192,3	K562	blood:
3	chr6:24645218..24647641-chr6:24665331..24668427,5	MCF-7	breast:
4	chr6:24645863..24648986-chr6:24665821..24668897,5	MCF-7	breast:
5	chr6:24646579..24649824-chr6:24666656..24668956,3	K562	blood:
6	chr6:24645396..24648552-chr6:24658188..24661192,4	K562	blood:
7	chr6:24645670..24648708-chr6:24654981..24659486,5	MCF-7	breast:

No data

Variant related genes	Relation type
KIAA0319	TF binding region
KIAA0319	CpG island
ENSG00000112308	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000111802	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12194181	0.86[CHB][hapmap]
rs3212231	0.86[CHB][hapmap]
rs6928074	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv601164	chr6:24625091-24661599	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv601165	chr6:24632642-24666007	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3756821	ACOT13	cis	cerebellum	SCAN
rs3756821	ACOT13	cis	parietal	SCAN
rs3756821	NKAPL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24643600-24647000	Active TSS	Fetal Brain Female	brain
2	chr6:24644000-24647000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:24644200-24647000	Active TSS	Brain Anterior Caudate	brain
4	chr6:24645400-24647000	Active TSS	Brain Angular Gyrus	brain
5	chr6:24645600-24647000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr6:24645600-24647000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr6:24645600-24647000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr6:24645600-24647000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:24645600-24647000	Active TSS	Brain Cingulate Gyrus	brain
10	chr6:24645600-24647000	Active TSS	Brain Hippocampus Middle	brain
11	chr6:24645600-24647000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:24645600-24647000	Flanking Active TSS	GM12878-XiMat	blood
13	chr6:24645600-24647000	Flanking Active TSS	NHEK	skin
14	chr6:24645800-24647000	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:24645800-24647000	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr6:24645800-24647000	Flanking Active TSS	Placenta	Placenta
17	chr6:24645800-24647000	Active TSS	Rectal Smooth Muscle	rectum
18	chr6:24645800-24647000	Enhancers	Small Intestine	intestine
19	chr6:24646000-24647000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr6:24646000-24647000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:24646000-24647000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:24646000-24647000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:24646000-24647000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:24646000-24647000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:24646000-24647000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:24646000-24647000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:24646000-24647000	Active TSS	Fetal Heart	heart
28	chr6:24646000-24647000	Active TSS	Stomach Smooth Muscle	stomach
29	chr6:24646000-24647200	Active TSS	Fetal Kidney	kidney
30	chr6:24646200-24647000	Active TSS	Primary T cells from cord blood	blood
31	chr6:24646200-24647000	Flanking Active TSS	Dnd41	blood
32	chr6:24646400-24647000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:24646400-24647000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr6:24646400-24647000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr6:24646400-24647000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr6:24646400-24647000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:24646400-24647000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:24646400-24647000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr6:24646400-24658800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr6:24646600-24647000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr6:24646600-24647000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr6:24646600-24647000	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr6:24646600-24647000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:24646600-24647000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr6:24646600-24647000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:24646600-24647000	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr6:24646600-24647000	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr6:24646600-24647000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr6:24646600-24647000	Enhancers	Stomach Mucosa	stomach
50	chr6:24646600-24647000	Flanking Active TSS	A549	lung

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