Variant report

Variant	rs3806325
Chromosome Location	chr1:221051792-221051793
allele	A/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	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	FOXM1	chr1:221051484-221051816	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:221051778-221053514	NB4	blood:	n/a	n/a
12	NFIC	chr1:221051392-221051912	GM12878	blood:	n/a	n/a
13	MEF2A	chr1:221051414-221051856	GM12878	blood:	n/a	chr1:221051680-221051701 chr1:221051680-221051701 chr1:221051680-221051701 chr1:221051685-221051699 chr1:221051686-221051697 chr1:221051684-221051700
14	BATF	chr1:221051370-221051859	GM12878	blood:	n/a	n/a
15	RUNX3	chr1:221051361-221052278	GM12878	blood:	n/a	n/a
16	NFIC	chr1:221051387-221051863	GM12878	blood:	n/a	n/a
17	SUZ12	chr1:221051729-221052684	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:221047152-221053823	HUVEC	blood vessel:	n/a	n/a
19	USF2	chr1:221051763-221052065	GM12878	blood:	n/a	n/a
20	USF1	chr1:221051640-221052087	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3A	chr1:221051745-221052917	H1-hESC	embryonic stem cell:	n/a	chr1:221051972-221051985 chr1:221051897-221051906 chr1:221052906-221052917
22	MEF2A	chr1:221051377-221051831	GM12878	blood:	n/a	chr1:221051680-221051701 chr1:221051680-221051701 chr1:221051680-221051701 chr1:221051685-221051699 chr1:221051686-221051697 chr1:221051684-221051700
23	ATF2	chr1:221051346-221051855	GM12878	blood:	n/a	n/a
24	MTA3	chr1:221051400-221051906	GM12878	blood:	n/a	n/a
25	MAX	chr1:221051751-221052135	H1-hESC	embryonic stem cell:	n/a	chr1:221051894-221051909
26	IKZF1	chr1:221051396-221051896	GM12878	blood:	n/a	chr1:221051633-221051641
27	MAX	chr1:221051631-221053170	NB4	blood:	n/a	chr1:221052899-221052909 chr1:221052464-221052473 chr1:221051894-221051909 chr1:221052603-221052613
28	MAX	chr1:221051727-221052406	H1-hESC	embryonic stem cell:	n/a	chr1:221051894-221051909
29	POLR2A	chr1:221051729-221051927	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr1:221051351-221053728	HL-60	blood:	n/a	n/a
31	POLR2A	chr1:221050386-221055418	H1-neurons	neurons:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:221051758-221051808	Caco-2	colon:	n/a
2	chr1:221051758-221051808	GM12878	blood:	n/a
3	chr1:221051758-221051808	NB4	blood:	n/a
4	chr1:221051758-221051808	BE2_C	brain:	n/a
5	chr1:221051758-221051808	ProgFib	skin:	n/a
6	chr1:221051758-221051808	A549	lung:	n/a
7	chr1:221051758-221051808	HCPEpiC	choroid plexus:	n/a
8	chr1:221051758-221051808	SKMC	muscle:	n/a
9	chr1:221051758-221051808	NT2-D1	testis:	n/a
10	chr1:221051758-221051808	HAEpiC	amniotic membrane:	n/a
11	chr1:221051758-221051808	NHDF-neo	bronchial:	n/a
12	chr1:221051758-221051808	HMEC	breast:	n/a
13	chr1:221051758-221051808	CMK	blood:	n/a
14	chr1:221051758-221051808	AoSMC	blood vessel:	n/a
15	chr1:221051758-221051808	HCT-116	colon:	n/a
16	chr1:221051758-221051808	SK-N-SH_RA	brain:	n/a
17	chr1:221051758-221051808	IMR90	lung:	fetal
18	chr1:221051758-221051808	HRE	kidney:	n/a
19	chr1:221051758-221051808	PFSK-1	brain:	n/a
20	chr1:221051758-221051808	SAEC	small airway:	n/a
21	chr1:221051758-221051808	HRPEpiC	eye:	n/a
22	chr1:221051758-221051808	LNCaP	prostate:	n/a
23	chr1:221051758-221051808	Hela-S3	cervix:	n/a
24	chr1:221051758-221051808	HEK293	kidney:	embryo
25	chr1:221051758-221051808	HRCEpiC	kidney:	n/a
26	chr1:221051758-221051808	BJ	skin:	n/a
27	chr1:221051758-221051808	GM12892	blood:	n/a
28	chr1:221051758-221051808	HNPCEpiC	eye:	n/a
29	chr1:221051758-221051808	AG04450	lung:	fetal
30	chr1:221051758-221051808	NHBE	bronchial:	n/a
31	chr1:221051758-221051808	AG04449	skin:	fetal
32	chr1:221051758-221051808	HUVEC	blood vessel:	n/a
33	chr1:221051758-221051808	K562	blood:	n/a
34	chr1:221051758-221051808	PrEC	prostate:	n/a
35	chr1:221051758-221051808	AG09309	skin:	n/a
36	chr1:221051758-221051808	AG09319	gingival:	n/a
37	chr1:221051758-221051808	HCM	heart:	n/a
38	chr1:221051758-221051808	RPTEC	kidney:	n/a
39	chr1:221051758-221051808	MCF10A-Er-Src	breast:	n/a
40	chr1:221051758-221051808	HEEpiC	esophagus:	n/a
41	chr1:221051758-221051808	T-47D	breast:	n/a
42	chr1:221051758-221051808	GM19239	blood:	n/a
43	chr1:221051758-221051808	H1-hESC	embryonic stem cell:	embryo
44	chr1:221051758-221051808	GM06990	blood:	n/a
45	chr1:221051758-221051808	SK-N-SH	brain:	n/a
46	chr1:221051758-221051808	HPAEpiC	pulmonary alveolar:	n/a
47	chr1:221051758-221051808	Hepatocyte	liver:	n/a
48	chr1:221051758-221051808	U87	brain:	n/a
49	chr1:221051758-221051808	SK-N-MC	brain:	n/a
50	chr1:221051758-221051808	PANC-1	pancreas:	n/a

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

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2184658	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[EUR][1000 genomes]
rs2247213	0.85[CHB][hapmap]
rs2738755	0.85[CHB][hapmap]
rs34180575	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35297838	1.00[LWK][hapmap]
rs3738182	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[TSI][hapmap];0.97[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3806325	KCTD3	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221046000-221051800	Weak transcription	Pancreas	Pancrea
2	chr1:221047800-221051800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:221048000-221051800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:221048000-221051800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:221048000-221052000	Weak transcription	A549	lung
6	chr1:221048400-221052000	Weak transcription	HSMMtube	muscle
7	chr1:221049000-221053800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:221049400-221052600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr1:221049600-221052600	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:221049600-221052800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:221049600-221052800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr1:221049600-221055600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:221049800-221052600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr1:221049800-221055400	Active TSS	Right Atrium	heart
15	chr1:221049800-221055800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:221050000-221051800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:221050000-221055400	Active TSS	Left Ventricle	heart
18	chr1:221050200-221051800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:221050200-221052000	Active TSS	Brain Hippocampus Middle	brain
20	chr1:221050200-221053800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr1:221050400-221052200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:221050400-221053600	Bivalent Enhancer	Fetal Brain Male	brain
23	chr1:221050400-221055200	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr1:221050600-221051800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
25	chr1:221050600-221051800	Enhancers	Brain Substantia Nigra	brain
26	chr1:221050600-221052000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
27	chr1:221050600-221052600	Enhancers	Spleen	Spleen
28	chr1:221050800-221051800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:221050800-221051800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr1:221050800-221051800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:221050800-221051800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr1:221050800-221051800	Bivalent Enhancer	Fetal Heart	heart
33	chr1:221050800-221052200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
34	chr1:221050800-221052600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr1:221051000-221051800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:221051000-221051800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
37	chr1:221051000-221051800	Bivalent Enhancer	Brain Germinal Matrix	brain
38	chr1:221051000-221051800	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:221051000-221051800	Weak transcription	Psoas Muscle	Psoas
40	chr1:221051000-221051800	Bivalent Enhancer	NH-A	brain
41	chr1:221051000-221051800	Enhancers	NHLF	lung
42	chr1:221051000-221052000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
43	chr1:221051000-221052000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:221051000-221052000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:221051000-221052000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
46	chr1:221051000-221052200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:221051000-221052200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:221051200-221051800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:221051200-221051800	Bivalent Enhancer	Placenta	Placenta
50	chr1:221051200-221051800	Bivalent Enhancer	Fetal Stomach	stomach

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