Variant report

Variant	rs3806324
Chromosome Location	chr1:221051924-221051925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr1:221051671-221052074	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr1:221051646-221052821	HL-60	blood:	n/a	chr1:221051972-221051985 chr1:221052190-221052204
3	RUNX3	chr1:221051368-221051942	GM12878	blood:	n/a	n/a
4	CTBP2	chr1:221049806-221056533	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:221049750-221054006	HL-60	blood:	n/a	n/a
6	USF2	chr1:221051781-221051983	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr1:221051657-221053132	NB4	blood:	n/a	chr1:221052899-221052909 chr1:221052464-221052473 chr1:221051894-221051909 chr1:221052603-221052613
8	SUZ12	chr1:221048843-221052557	NT2-D1	testis:	n/a	n/a
9	POLR2A	chr1:221050359-221052771	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr1:221051778-221053514	NB4	blood:	n/a	n/a
11	MXI1	chr1:221051833-221056348	IMR90	lung:	n/a	chr1:221051897-221051906
12	RUNX3	chr1:221051361-221052278	GM12878	blood:	n/a	n/a
13	SUZ12	chr1:221051729-221052684	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:221047152-221053823	HUVEC	blood vessel:	n/a	n/a
15	USF2	chr1:221051763-221052065	GM12878	blood:	n/a	n/a
16	CTCF	chr1:221051920-221052070	NHLF	lung:	n/a	n/a
17	USF1	chr1:221051640-221052087	H1-hESC	embryonic stem cell:	n/a	n/a
18	SIN3A	chr1:221051745-221052917	H1-hESC	embryonic stem cell:	n/a	chr1:221051972-221051985 chr1:221051897-221051906 chr1:221052906-221052917
19	MAX	chr1:221051751-221052135	H1-hESC	embryonic stem cell:	n/a	chr1:221051894-221051909
20	MAX	chr1:221051631-221053170	NB4	blood:	n/a	chr1:221052899-221052909 chr1:221052464-221052473 chr1:221051894-221051909 chr1:221052603-221052613
21	MAX	chr1:221051727-221052406	H1-hESC	embryonic stem cell:	n/a	chr1:221051894-221051909
22	POLR2A	chr1:221051729-221051927	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr1:221051351-221053728	HL-60	blood:	n/a	n/a
24	POLR2A	chr1:221050386-221055418	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	chr1:221051907-221051957	AG04449	skin:	fetal
2	chr1:221051907-221051957	AG04450	lung:	fetal
3	chr1:221051907-221051957	BE2_C	brain:	n/a
4	chr1:221051907-221051957	GM06990	blood:	n/a
5	chr1:221051907-221051957	A549	lung:	n/a
6	chr1:221051907-221051957	HAEpiC	amniotic membrane:	n/a
7	chr1:221051907-221051957	GM12892	blood:	n/a
8	chr1:221051907-221051957	PFSK-1	brain:	n/a
9	chr1:221051907-221051957	LNCaP	prostate:	n/a
10	chr1:221051907-221051957	GM19239	blood:	n/a
11	chr1:221051907-221051957	NHDF-neo	bronchial:	n/a
12	chr1:221051907-221051957	HCPEpiC	choroid plexus:	n/a
13	chr1:221051907-221051957	HIPEpiC	eye:	n/a
14	chr1:221051907-221051957	SK-N-SH_RA	brain:	n/a
15	chr1:221051907-221051957	AG09319	gingival:	n/a
16	chr1:221051907-221051957	SKMC	muscle:	n/a
17	chr1:221051907-221051957	SK-N-SH	brain:	n/a
18	chr1:221051907-221051957	RPTEC	kidney:	n/a
19	chr1:221051907-221051957	HCF	heart:	n/a
20	chr1:221051907-221051957	HRE	kidney:	n/a
21	chr1:221051907-221051957	SAEC	small airway:	n/a
22	chr1:221051907-221051957	HepG2	liver:	n/a
23	chr1:221051907-221051957	K562	blood:	n/a
24	chr1:221051907-221051957	CMK	blood:	n/a
25	chr1:221051907-221051957	ECC-1	luminal epithelium:	n/a
26	chr1:221051907-221051957	HCT-116	colon:	n/a
27	chr1:221051907-221051957	HNPCEpiC	eye:	n/a
28	chr1:221051907-221051957	AoSMC	blood vessel:	n/a
29	chr1:221051907-221051957	IMR90	lung:	fetal
30	chr1:221051907-221051957	ovcar-3	ovarian:	n/a
31	chr1:221051907-221051957	HMEC	breast:	n/a
32	chr1:221051907-221051957	PANC-1	pancreas:	n/a
33	chr1:221051907-221051957	PrEC	prostate:	n/a
34	chr1:221051907-221051957	Jurkat	blood:	n/a
35	chr1:221051907-221051957	AG09309	skin:	n/a
36	chr1:221051907-221051957	HRPEpiC	eye:	n/a
37	chr1:221051907-221051957	HPAEpiC	pulmonary alveolar:	n/a
38	chr1:221051907-221051957	HUVEC	blood vessel:	n/a
39	chr1:221051907-221051957	Hela-S3	cervix:	n/a
40	chr1:221051907-221051957	MCF10A-Er-Src	breast:	n/a
41	chr1:221051907-221051957	NB4	blood:	n/a
42	chr1:221051907-221051957	NHBE	bronchial:	n/a
43	chr1:221051907-221051957	SK-N-MC	brain:	n/a
44	chr1:221051907-221051957	Caco-2	colon:	n/a
45	chr1:221051907-221051957	GM12878	blood:	n/a
46	chr1:221051907-221051957	MCF-7	breast:	n/a
47	chr1:221051907-221051957	HEEpiC	esophagus:	n/a
48	chr1:221051907-221051957	GM12891	blood:	n/a
49	chr1:221051907-221051957	BJ	skin:	n/a
50	chr1:221051907-221051957	AG10803	skin:	n/a

No data

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

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12031225	1.00[JPT][hapmap]
rs2807866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs60455465	0.86[ASN][1000 genomes]
rs7339930	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140842	0.86[ASN][1000 genomes]

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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv1798350	chr1:221020278-221069740	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3393770	chr1:221051854-221054702	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221048000-221052000	Weak transcription	A549	lung
2	chr1:221048400-221052000	Weak transcription	HSMMtube	muscle
3	chr1:221049000-221053800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:221049400-221052600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr1:221049600-221052600	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr1:221049600-221052800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:221049600-221052800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr1:221049600-221055600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:221049800-221052600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
10	chr1:221049800-221055400	Active TSS	Right Atrium	heart
11	chr1:221049800-221055800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:221050000-221055400	Active TSS	Left Ventricle	heart
13	chr1:221050200-221052000	Active TSS	Brain Hippocampus Middle	brain
14	chr1:221050200-221053800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr1:221050400-221052200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:221050400-221053600	Bivalent Enhancer	Fetal Brain Male	brain
17	chr1:221050400-221055200	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr1:221050600-221052000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
19	chr1:221050600-221052600	Enhancers	Spleen	Spleen
20	chr1:221050800-221052200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr1:221050800-221052600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr1:221051000-221052000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
23	chr1:221051000-221052000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:221051000-221052000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:221051000-221052000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
26	chr1:221051000-221052200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:221051000-221052200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:221051200-221052200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:221051200-221052200	Bivalent Enhancer	Stomach Mucosa	stomach
30	chr1:221051200-221052400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:221051200-221052600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
32	chr1:221051200-221053800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
33	chr1:221051200-221054400	Active TSS	Lung	lung
34	chr1:221051200-221055000	Active TSS	Rectal Smooth Muscle	rectum
35	chr1:221051200-221055600	Active TSS	Right Ventricle	heart
36	chr1:221051400-221052000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
37	chr1:221051400-221052200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr1:221051400-221052800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
39	chr1:221051400-221054000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
40	chr1:221051400-221056000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
41	chr1:221051600-221052000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:221051600-221052000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
43	chr1:221051600-221052000	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:221051600-221052000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
45	chr1:221051600-221052000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
46	chr1:221051600-221052000	Bivalent Enhancer	Fetal Thymus	thymus
47	chr1:221051600-221052000	Flanking Active TSS	NHDF-Ad	bronchial
48	chr1:221051600-221052200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:221051600-221052200	Flanking Active TSS	Osteobl	bone
50	chr1:221051600-221052400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood

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