Variant report

Variant	rs949994
Chromosome Location	chr1:221054379-221054380
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr1:221054278-221054544	GM12878	blood:	n/a	n/a
2	CTBP2	chr1:221049806-221056533	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:221052138-221055250	IMR90	lung:	n/a	n/a
4	KAP1	chr1:221054325-221054991	HEK293	kidney:	n/a	chr1:221054847-221054855
5	SIN3A	chr1:221054276-221054830	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr1:221054350-221054984	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:221054246-221054387	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:221054124-221056451	HUVEC	blood vessel:	n/a	n/a
9	MAZ	chr1:221051935-221057120	IMR90	lung:	n/a	chr1:221052899-221052909 chr1:221052464-221052473 chr1:221052603-221052613
10	SUZ12	chr1:221054227-221056121	H1-hESC	embryonic stem cell:	n/a	n/a
11	CHD1	chr1:221054327-221054530	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr1:221051833-221056348	IMR90	lung:	n/a	chr1:221051897-221051906
13	POLR2A	chr1:221052825-221055075	H1-neurons	neurons:	n/a	n/a
14	SUZ12	chr1:221052903-221055995	NT2-D1	testis:	n/a	n/a
15	MXI1	chr1:221054287-221054739	H1-hESC	embryonic stem cell:	n/a	n/a
16	SP1	chr1:221054175-221054637	H1-hESC	embryonic stem cell:	n/a	chr1:221054452-221054466
17	POLR2A	chr1:221054077-221056927	HL-60	blood:	n/a	n/a
18	POLR2A	chr1:221054051-221054973	HL-60	blood:	n/a	n/a
19	SP1	chr1:221054130-221054701	H1-hESC	embryonic stem cell:	n/a	chr1:221054452-221054466
20	POLR2A	chr1:221053912-221054405	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr1:221050386-221055418	H1-neurons	neurons:	n/a	n/a
22	MAX	chr1:221054073-221054420	K562	blood:	n/a	n/a
23	BACH1	chr1:221054256-221054601	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:221054365-221054415	GM06990	blood:	n/a
2	chr1:221054365-221054415	GM12892	blood:	n/a
3	chr1:221054365-221054415	NHBE	bronchial:	n/a
4	chr1:221054365-221054415	BE2_C	brain:	n/a
5	chr1:221054365-221054415	AoSMC	blood vessel:	n/a
6	chr1:221054365-221054415	NH-A	brain:	n/a
7	chr1:221054365-221054415	Hepatocyte	liver:	n/a
8	chr1:221054365-221054415	LNCaP	prostate:	n/a
9	chr1:221054365-221054415	SAEC	small airway:	n/a
10	chr1:221054365-221054415	HMEC	breast:	n/a
11	chr1:221054365-221054415	GM12878	blood:	n/a
12	chr1:221054365-221054415	SK-N-SH	brain:	n/a
13	chr1:221054365-221054415	GM19239	blood:	n/a
14	chr1:221054365-221054415	A549	lung:	n/a
15	chr1:221054365-221054415	NT2-D1	testis:	n/a
16	chr1:221054365-221054415	ProgFib	skin:	n/a
17	chr1:221054365-221054415	NHDF-neo	bronchial:	n/a
18	chr1:221054365-221054415	AG04450	lung:	fetal
19	chr1:221054365-221054415	Hela-S3	cervix:	n/a
20	chr1:221054365-221054415	HEK293	kidney:	embryo
21	chr1:221054365-221054415	HRPEpiC	eye:	n/a
22	chr1:221054365-221054415	Caco-2	colon:	n/a
23	chr1:221054365-221054415	HCPEpiC	choroid plexus:	n/a
24	chr1:221054365-221054415	Jurkat	blood:	n/a
25	chr1:221054365-221054415	MCF-7	breast:	n/a
26	chr1:221054365-221054415	GM12891	blood:	n/a
27	chr1:221054365-221054415	HAEpiC	amniotic membrane:	n/a
28	chr1:221054365-221054415	HEEpiC	esophagus:	n/a
29	chr1:221054365-221054415	HRE	kidney:	n/a
30	chr1:221054365-221054415	HCT-116	colon:	n/a
31	chr1:221054365-221054415	CMK	blood:	n/a
32	chr1:221054365-221054415	RPTEC	kidney:	n/a
33	chr1:221054365-221054415	SKMC	muscle:	n/a
34	chr1:221054365-221054415	PFSK-1	brain:	n/a
35	chr1:221054365-221054415	K562	blood:	n/a
36	chr1:221054365-221054415	AG09309	skin:	n/a
37	chr1:221054365-221054415	BJ	skin:	n/a
38	chr1:221054365-221054415	SK-N-MC	brain:	n/a
39	chr1:221054365-221054415	IMR90	lung:	fetal
40	chr1:221054365-221054415	PANC-1	pancreas:	n/a
41	chr1:221054365-221054415	HIPEpiC	eye:	n/a
42	chr1:221054365-221054415	HL-60	blood:	n/a
43	chr1:221054365-221054415	HNPCEpiC	eye:	n/a
44	chr1:221054365-221054415	AG09319	gingival:	n/a
45	chr1:221054365-221054415	HCF	heart:	n/a
46	chr1:221054365-221054415	HCM	heart:	n/a
47	chr1:221054365-221054415	HUVEC	blood vessel:	n/a
48	chr1:221054365-221054415	NB4	blood:	n/a
49	chr1:221054365-221054415	PrEC	prostate:	n/a
50	chr1:221054365-221054415	AG04449	skin:	fetal

No data

Variant related genes	Relation type
HLX	TF binding region
HLA-AS1	TF binding region
HLA-AS1	CpG island
HLX	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1537804	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1537805	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17009074	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2184658	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2484707	1.00[EUR][1000 genomes]
rs2784250	0.94[ASN][1000 genomes]
rs2807862	0.94[ASN][1000 genomes]
rs3738182	0.86[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs4846672	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55955117	1.00[EUR][1000 genomes]
rs56953379	1.00[EUR][1000 genomes]
rs57651577	1.00[EUR][1000 genomes]
rs58040980	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60458871	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60757003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6682092	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73097473	1.00[EUR][1000 genomes]
rs73102740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73108360	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73108374	1.00[EUR][1000 genomes]
rs7550867	1.00[EUR][1000 genomes]
rs950635	0.94[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs949994	TSC22D1	trans	lymphoblastoid	seeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221049600-221055600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:221049800-221055400	Active TSS	Right Atrium	heart
3	chr1:221049800-221055800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:221050000-221055400	Active TSS	Left Ventricle	heart
5	chr1:221050400-221055200	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr1:221051200-221054400	Active TSS	Lung	lung
7	chr1:221051200-221055000	Active TSS	Rectal Smooth Muscle	rectum
8	chr1:221051200-221055600	Active TSS	Right Ventricle	heart
9	chr1:221051400-221056000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
10	chr1:221051600-221054400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:221051600-221054600	Active TSS	Colon Smooth Muscle	Colon
12	chr1:221051800-221055200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:221051800-221055800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:221052000-221054800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr1:221052000-221054800	Bivalent/Poised TSS	Thymus	Thymus
16	chr1:221052000-221054800	Active TSS	HSMM	muscle
17	chr1:221052000-221054800	Active TSS	HSMMtube	muscle
18	chr1:221052000-221055000	Bivalent/Poised TSS	Fetal Lung	lung
19	chr1:221052000-221055000	Active TSS	Ovary	ovary
20	chr1:221052000-221055000	Active TSS	NHDF-Ad	bronchial
21	chr1:221052000-221055400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:221052000-221055600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:221052000-221055800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
24	chr1:221052000-221055800	Active TSS	Psoas Muscle	Psoas
25	chr1:221052000-221058000	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr1:221052200-221054400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:221052200-221054600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr1:221052200-221055200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:221052200-221055400	Active TSS	NHLF	lung
30	chr1:221052200-221055400	Active TSS	Osteobl	bone
31	chr1:221052200-221055800	Active TSS	Brain Substantia Nigra	brain
32	chr1:221052400-221054400	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr1:221052400-221054600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:221052400-221054800	Bivalent/Poised TSS	Fetal Kidney	kidney
35	chr1:221052400-221055200	Active TSS	Brain Hippocampus Middle	brain
36	chr1:221052400-221055400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:221052400-221056600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
38	chr1:221052600-221054800	Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr1:221052600-221055000	Active TSS	Primary monocytes fromperipheralblood	blood
40	chr1:221052600-221055000	Bivalent/Poised TSS	Small Intestine	intestine
41	chr1:221052600-221055400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
42	chr1:221052600-221055800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:221052600-221056400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
44	chr1:221052800-221055000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
45	chr1:221052800-221055000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
46	chr1:221052800-221055000	Active TSS	Monocytes-CD14+_RO01746	blood
47	chr1:221053000-221055800	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr1:221053400-221054800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:221053400-221054800	Bivalent/Poised TSS	Esophagus	oesophagus
50	chr1:221053400-221055000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus

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