Variant report

Variant	rs6674275
Chromosome Location	chr1:227936460-227936461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:227936273-227937013	K562	blood:	n/a	n/a
2	EP300	chr1:227936422-227936966	K562	blood:	n/a	n/a
3	POLR2A	chr1:227934449-227938226	PBDE	blood:	n/a	n/a
4	ARID3A	chr1:227936375-227936901	K562	blood:	n/a	n/a
5	RCOR1	chr1:227936248-227936902	K562	blood:	n/a	n/a
6	CREB1	chr1:227936049-227936749	K562	blood:	n/a	n/a
7	JUND	chr1:227936206-227937051	K562	blood:	n/a	n/a
8	USF1	chr1:227936153-227936517	K562	blood:	n/a	n/a
9	GATA1	chr1:227936047-227937257	PBDE	blood:	n/a	n/a
10	MAZ	chr1:227936283-227936972	K562	blood:	n/a	n/a
11	ATF1	chr1:227936182-227936966	K562	blood:	n/a	n/a
12	TBL1XR1	chr1:227936279-227936998	K562	blood:	n/a	n/a
13	MAFK	chr1:227936287-227936863	K562	blood:	n/a	n/a
14	TEAD4	chr1:227936197-227937010	K562	blood:	n/a	chr1:227936268-227936277
15	MAX	chr1:227936204-227936938	K562	blood:	n/a	n/a
16	RCOR1	chr1:227936190-227937021	K562	blood:	n/a	n/a
17	PML	chr1:227936373-227936894	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:227923199..227926110-chr1:227936380..227938690,2	K562	blood:
2	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
3	chr1:227936020..227939973-chr1:227940260..227944026,6	K562	blood:

No data

Variant related genes	Relation type
SNAP47-AS1	TF binding region
ENSG00000143740	Chromatin interaction
ENSG00000081692	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12064596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376549	0.86[CHB][hapmap]
rs16848112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2093611	0.86[CHB][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236358	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273938	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57892813	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61521615	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679352	0.82[CHB][hapmap]
rs6688900	0.80[AMR][1000 genomes]
rs6695545	0.82[AMR][1000 genomes]
rs66969031	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704268	0.82[CHB][hapmap]
rs67502955	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72632835	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72632836	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555241	0.95[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227924200-227940800	Weak transcription	HSMMtube	muscle
2	chr1:227924200-227941200	Weak transcription	HSMM	muscle
3	chr1:227924200-227941200	Weak transcription	NHDF-Ad	bronchial
4	chr1:227924200-227941600	Weak transcription	Osteobl	bone
5	chr1:227924200-227942000	Weak transcription	Hela-S3	cervix
6	chr1:227924200-227946800	Weak transcription	HUVEC	blood vessel
7	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:227924800-227941400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:227925000-227941400	Weak transcription	Fetal Brain Male	brain
10	chr1:227925200-227941200	Weak transcription	Psoas Muscle	Psoas
11	chr1:227925600-227941800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:227928600-227941200	Weak transcription	Small Intestine	intestine
13	chr1:227930200-227945600	Weak transcription	NH-A	brain
14	chr1:227930400-227939400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:227931800-227938400	Weak transcription	NHEK	skin
16	chr1:227932800-227941400	Weak transcription	Stomach Mucosa	stomach
17	chr1:227932800-227947200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:227933000-227939400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:227933000-227946400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:227933800-227939000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:227934000-227938600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr1:227934000-227940200	Strong transcription	Thymus	Thymus
23	chr1:227934000-227941400	Strong transcription	Fetal Brain Female	brain
24	chr1:227934000-227948800	Strong transcription	Primary T cells from cord blood	blood
25	chr1:227934200-227945400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:227934400-227937000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr1:227934400-227938400	Genic enhancers	Fetal Stomach	stomach
28	chr1:227934400-227939600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:227934400-227950000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:227934600-227942600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:227934600-227942800	Strong transcription	Brain Germinal Matrix	brain
32	chr1:227934800-227937600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:227934800-227941200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:227934800-227943200	Strong transcription	Fetal Intestine Large	intestine
35	chr1:227934800-227950200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:227934800-227950400	Strong transcription	Fetal Intestine Small	intestine
37	chr1:227935000-227937200	Enhancers	Colon Smooth Muscle	Colon
38	chr1:227935000-227937200	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:227935000-227937400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:227935000-227938000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:227935000-227938800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:227935000-227939200	Genic enhancers	Gastric	stomach
43	chr1:227935000-227939400	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:227935000-227939400	Genic enhancers	Right Ventricle	heart
45	chr1:227935000-227939600	Strong transcription	NHLF	lung
46	chr1:227935000-227942600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:227935000-227949600	Strong transcription	Dnd41	blood
48	chr1:227935200-227936800	Strong transcription	Spleen	Spleen
49	chr1:227935200-227937400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:227935200-227937400	Genic enhancers	Duodenum Mucosa	Duodenum

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