Variant report

Variant	rs2295222
Chromosome Location	chr14:37126308-37126309
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr14:37123241-37129363	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr14:37125132-37130861	NT2-D1	testis:	n/a	n/a
3	POLR2A	chr14:37125220-37126347	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	chr14:37126283-37126333	AG04449	skin:	fetal
2	chr14:37126283-37126333	HMEC	breast:	n/a
3	chr14:37126283-37126333	HRCEpiC	kidney:	n/a
4	chr14:37126283-37126333	BE2_C	brain:	n/a
5	chr14:37126283-37126333	Hepatocyte	liver:	n/a
6	chr14:37126283-37126333	HCM	heart:	n/a
7	chr14:37126283-37126333	PrEC	prostate:	n/a
8	chr14:37126283-37126333	HNPCEpiC	eye:	n/a
9	chr14:37126283-37126333	PANC-1	pancreas:	n/a
10	chr14:37126283-37126333	AG09309	skin:	n/a
11	chr14:37126283-37126333	Jurkat	blood:	n/a
12	chr14:37126283-37126333	ProgFib	skin:	n/a
13	chr14:37126283-37126333	CMK	blood:	n/a
14	chr14:37126283-37126333	RPTEC	kidney:	n/a
15	chr14:37126283-37126333	BJ	skin:	n/a
16	chr14:37126283-37126333	HPAEpiC	pulmonary alveolar:	n/a
17	chr14:37126283-37126333	A549	lung:	n/a
18	chr14:37126283-37126333	SKMC	muscle:	n/a
19	chr14:37126283-37126333	HCF	heart:	n/a
20	chr14:37126283-37126333	SK-N-SH	brain:	n/a
21	chr14:37126283-37126333	NB4	blood:	n/a
22	chr14:37126283-37126333	GM12878	blood:	n/a
23	chr14:37126283-37126333	HCPEpiC	choroid plexus:	n/a
24	chr14:37126283-37126333	HEEpiC	esophagus:	n/a
25	chr14:37126283-37126333	AoSMC	blood vessel:	n/a
26	chr14:37126283-37126333	HL-60	blood:	n/a
27	chr14:37126283-37126333	HEK293	kidney:	embryo
28	chr14:37126283-37126333	SAEC	small airway:	n/a
29	chr14:37126283-37126333	Hela-S3	cervix:	n/a
30	chr14:37126283-37126333	NH-A	brain:	n/a
31	chr14:37126283-37126333	K562	blood:	n/a
32	chr14:37126283-37126333	U87	brain:	n/a
33	chr14:37126283-37126333	AG09319	gingival:	n/a
34	chr14:37126283-37126333	GM06990	blood:	n/a
35	chr14:37126283-37126333	GM12892	blood:	n/a
36	chr14:37126283-37126333	T-47D	breast:	n/a
37	chr14:37126283-37126333	IMR90	lung:	fetal
38	chr14:37126283-37126333	HepG2	liver:	n/a
39	chr14:37126283-37126333	HUVEC	blood vessel:	n/a
40	chr14:37126283-37126333	MCF10A-Er-Src	breast:	n/a
41	chr14:37126283-37126333	SK-N-MC	brain:	n/a
42	chr14:37126283-37126333	HIPEpiC	eye:	n/a
43	chr14:37126283-37126333	Caco-2	colon:	n/a
44	chr14:37126283-37126333	HRPEpiC	eye:	n/a
45	chr14:37126283-37126333	LNCaP	prostate:	n/a
46	chr14:37126283-37126333	H1-hESC	embryonic stem cell:	embryo
47	chr14:37126283-37126333	HRE	kidney:	n/a
48	chr14:37126283-37126333	NHBE	bronchial:	n/a
49	chr14:37126283-37126333	GM12891	blood:	n/a
50	chr14:37126283-37126333	NHDF-neo	bronchial:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:37123470..37126797-chr14:37128985..37133128,4	MCF-7	breast:

No data

Variant related genes	Relation type
PAX9	TF binding region
PAX9	CpG island
ENSG00000198807	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1016788	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11623821	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11627979	0.89[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs1950363	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2415353	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34070426	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35122436	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58039807	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61994901	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61994920	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140425	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7142363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723617	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72679708	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040256	chr14:36501452-37172046	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv542040	chr14:36501452-37172046	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv1047290	chr14:36564568-37445157	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv1037952	chr14:36670484-37294692	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv542042	chr14:36670484-37294692	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv1053685	chr14:36915643-37245920	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv917279	chr14:36953511-37146655	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2295222	FOXA1	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:37123400-37130800	Bivalent/Poised TSS	Fetal Thymus	thymus
2	chr14:37123400-37132000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr14:37123600-37126400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
4	chr14:37123600-37128200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
5	chr14:37123800-37126400	Bivalent Enhancer	Left Ventricle	heart
6	chr14:37123800-37128000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
7	chr14:37124000-37126400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr14:37124200-37126400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
9	chr14:37124200-37126800	Enhancers	Pancreas	Pancrea
10	chr14:37124400-37127200	Bivalent Enhancer	Placenta	Placenta
11	chr14:37124800-37126400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr14:37125000-37127000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
13	chr14:37125000-37128000	Bivalent Enhancer	Liver	Liver
14	chr14:37125000-37130800	Bivalent/Poised TSS	Thymus	Thymus
15	chr14:37125200-37126800	Bivalent Enhancer	Fetal Heart	heart
16	chr14:37125200-37126800	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr14:37125200-37127200	Active TSS	Right Atrium	heart
18	chr14:37125200-37128000	Bivalent Enhancer	Fetal Brain Male	brain
19	chr14:37125400-37126400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
20	chr14:37125400-37126800	Bivalent Enhancer	Brain Angular Gyrus	brain
21	chr14:37125400-37126800	Bivalent Enhancer	Fetal Intestine Small	intestine
22	chr14:37125400-37127400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
23	chr14:37125400-37127600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
24	chr14:37125600-37126600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr14:37125600-37126600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
26	chr14:37125600-37126800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr14:37125600-37126800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:37125600-37126800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr14:37125600-37126800	Bivalent Enhancer	Brain Germinal Matrix	brain
30	chr14:37125600-37126800	Bivalent Enhancer	Fetal Stomach	stomach
31	chr14:37125600-37127200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
32	chr14:37125800-37126400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
33	chr14:37125800-37126400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
34	chr14:37125800-37126400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr14:37125800-37126400	Bivalent Enhancer	Gastric	stomach
36	chr14:37125800-37126600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr14:37125800-37126600	Bivalent Enhancer	Colon Smooth Muscle	Colon
38	chr14:37126000-37126400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
39	chr14:37126000-37126400	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
40	chr14:37126000-37126400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
41	chr14:37126000-37127200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
42	chr14:37126000-37127400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr14:37126000-37127400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr14:37126200-37126400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr14:37126200-37126400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr14:37126200-37126400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
47	chr14:37126200-37126400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr14:37126200-37126400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr14:37126200-37126400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
50	chr14:37126200-37126400	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain

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