Variant report

Variant	rs4244626
Chromosome Location	chr1:246936665-246936666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
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	CREB1	chr1:246936369-246936938	GM12878	blood:	n/a	n/a
2	MAX	chr1:246936596-246936941	GM12878	blood:	n/a	n/a
3	PAX5	chr1:246936504-246936865	GM12878	blood:	n/a	n/a
4	MAX	chr1:246936600-246937002	MCF-7	breast:	n/a	n/a
5	GATA3	chr1:246936639-246937182	MCF-7	breast:	n/a	n/a
6	POU2F2	chr1:246936302-246936965	GM12878	blood:	n/a	n/a
7	NFIC	chr1:246936461-246936937	GM12878	blood:	n/a	n/a
8	GATA3	chr1:246936663-246937098	MCF-7	breast:	n/a	n/a
9	SP1	chr1:246936352-246936786	GM12878	blood:	n/a	n/a
10	RCOR1	chr1:246936388-246936798	GM12878	blood:	n/a	n/a
11	RUNX3	chr1:246936319-246936893	GM12878	blood:	n/a	n/a
12	POU2F2	chr1:246936495-246936713	GM12878	blood:	n/a	n/a
13	MAZ	chr1:246936375-246936760	GM12878	blood:	n/a	n/a
14	PAX5	chr1:246936546-246936859	GM12878	blood:	n/a	n/a
15	PAX5	chr1:246936402-246936990	GM12878	blood:	n/a	n/a
16	POU2F2	chr1:246936405-246936830	GM12891	blood:	n/a	n/a
17	RUNX3	chr1:246936292-246936847	GM12878	blood:	n/a	n/a
18	SP1	chr1:246936337-246936798	GM12878	blood:	n/a	n/a
19	POU2F2	chr1:246936357-246936859	GM12878	blood:	n/a	n/a
20	POU2F2	chr1:246936336-246936864	GM12891	blood:	n/a	n/a
21	SPI1	chr1:246936458-246936736	GM12891	blood:	n/a	n/a
22	BCLAF1	chr1:246936225-246936868	GM12878	blood:	n/a	n/a
23	EP300	chr1:246936355-246936768	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246933982..246937125-chr1:246938877..246940973,4	K562	blood:
2	chr1:246935414..246937125-chr1:246938877..246940791,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCCPDH-1	chr1:246935603-246939074	ENSG00000260855.1
2	lnc-SCCPDH-1	chr1:246935607-246937461	NONHSAT010724

No data

Variant related genes	Relation type
ENSG00000227953	TF binding region
ENSG00000227953	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10732299	1.00[AMR][1000 genomes]
rs10924822	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12040914	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069175	1.00[AMR][1000 genomes]
rs12071299	1.00[AMR][1000 genomes]
rs12119414	1.00[CHD][hapmap]
rs1691257	1.00[AMR][1000 genomes]
rs1779973	1.00[AMR][1000 genomes]
rs1779976	1.00[AMR][1000 genomes]
rs2800223	1.00[AMR][1000 genomes]
rs2996552	1.00[AMR][1000 genomes]
rs3007320	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3007321	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3007325	1.00[AMR][1000 genomes]
rs3007326	0.81[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3007327	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3122533	1.00[AMR][1000 genomes]
rs4244625	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4244629	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4244631	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4511163	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4532864	1.00[ASW][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4926452	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4926463	1.00[AMR][1000 genomes]
rs6426335	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6663093	1.00[AMR][1000 genomes]
rs6696798	1.00[AMR][1000 genomes]
rs7416659	1.00[AMR][1000 genomes]
rs923972	1.00[AMR][1000 genomes]
rs9426266	1.00[AMR][1000 genomes]
rs9426274	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv549545	chr1:246936353-246963019	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
5	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
8	chr1:246920800-246944200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:246921200-246943200	Strong transcription	Dnd41	blood
10	chr1:246921600-246945800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:246922200-246937000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:246922200-246944600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:246923200-246945000	Strong transcription	Fetal Muscle Leg	muscle
14	chr1:246924000-246941200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:246924000-246944200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:246924400-246939200	Weak transcription	Colonic Mucosa	Colon
17	chr1:246924400-246945800	Weak transcription	Primary B cells from cord blood	blood
18	chr1:246925200-246952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:246926400-246939200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:246928600-246937000	Strong transcription	Fetal Stomach	stomach
21	chr1:246928800-246944800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:246929200-246936800	Strong transcription	Fetal Brain Female	brain
23	chr1:246930600-246939000	Weak transcription	Thymus	Thymus
24	chr1:246931000-246936800	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr1:246931200-246937800	Weak transcription	NH-A	brain
26	chr1:246931200-246940600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:246932000-246939200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:246932400-246939000	Weak transcription	Pancreas	Pancrea
29	chr1:246932400-246945800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:246932400-246952000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:246932600-246938600	Weak transcription	Brain Substantia Nigra	brain
32	chr1:246932600-246939200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:246932600-246939400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:246932600-246948000	Strong transcription	Liver	Liver
35	chr1:246932600-246948600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:246932600-246948600	Weak transcription	Esophagus	oesophagus
37	chr1:246932800-246937800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:246932800-246938400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:246932800-246938600	Weak transcription	HUVEC	blood vessel
40	chr1:246932800-246938600	Weak transcription	Osteobl	bone
41	chr1:246932800-246939000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:246932800-246939200	Weak transcription	Brain Angular Gyrus	brain
43	chr1:246932800-246939200	Weak transcription	Gastric	stomach
44	chr1:246932800-246939200	Weak transcription	Spleen	Spleen
45	chr1:246932800-246939400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:246932800-246939400	Weak transcription	NHLF	lung
47	chr1:246932800-246945000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:246932800-246945600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:246932800-246945800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:246932800-246948800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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