Variant report

Variant	rs4650041
Chromosome Location	chr1:70821307-70821308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:70819053-70821497	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70686799..70688622-chr1:70819236..70822047,3	K562	blood:
2	chr1:70670191..70673421-chr1:70819814..70822311,3	K562	blood:
3	chr1:70819015..70821620-chr1:70875663..70878848,3	MCF-7	breast:
4	chr1:70819013..70822302-chr1:70824014..70829303,9	MCF-7	breast:
5	chr1:70820419..70821379-chr6:31794911..31795554,2	Hela-S3	cervix:
6	chr1:70685799..70687948-chr1:70819964..70821804,2	MCF-7	breast:
7	chr1:70686924..70688596-chr1:70820161..70821739,2	MCF-7	breast:
8	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:
9	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:

No data

Variant related genes	Relation type
ANKRD13C	TF binding region
ENSG00000066557	Chromatin interaction
ENSG00000116761	Chromatin interaction
ENSG00000228988	Chromatin interaction
ENSG00000116754	Chromatin interaction
ENSG00000204388	Chromatin interaction
ENSG00000226088	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10465863	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10889868	0.86[CHD][hapmap]
rs11209599	1.00[CEU][hapmap]
rs11209600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11209602	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11209603	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11209605	0.82[CHD][hapmap]
rs11209608	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11209611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11800138	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12028257	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12029977	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12030275	0.88[CEU][hapmap];0.88[AMR][1000 genomes]
rs12031053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12034101	0.86[AMR][1000 genomes]
rs12036256	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];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12037272	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];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12042565	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565458	0.88[AMR][1000 genomes]
rs12565460	0.86[AMR][1000 genomes]
rs1327873	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes]
rs17131276	0.83[CEU][hapmap];0.86[AMR][1000 genomes]
rs17131285	0.83[CEU][hapmap];0.86[AMR][1000 genomes]
rs1969953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4560989	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4650038	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4650047	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes]
rs56211824	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58997663	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59821213	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60602940	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61122312	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61587863	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61678482	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6686181	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72678630	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72678644	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72678645	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72678646	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72680732	0.86[AMR][1000 genomes]
rs7539544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs768433	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs998523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	esv11736	chr1:70820591-70825114	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4650041	SFRS11	Cis_1M	lymphoblastoid	RTeQTL
rs4650041	HHLA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70817600-70821400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:70817600-70821600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr1:70817600-70822000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:70817800-70821400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:70818000-70821400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:70818000-70821400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:70818000-70821400	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:70818000-70821800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:70818200-70821400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:70818200-70821400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:70818200-70821400	Active TSS	A549	lung
12	chr1:70818400-70821400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:70818800-70821400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:70819000-70821400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr1:70819400-70821400	Active TSS	Rectal Smooth Muscle	rectum
16	chr1:70820400-70821400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:70820600-70821400	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:70820600-70821400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr1:70820600-70821400	Flanking Active TSS	Dnd41	blood
20	chr1:70820600-70821400	Flanking Active TSS	NH-A	brain
21	chr1:70820800-70821400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr1:70820800-70821400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:70820800-70821400	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr1:70820800-70821400	Flanking Active TSS	GM12878-XiMat	blood
25	chr1:70820800-70821400	Flanking Active TSS	Hela-S3	cervix
26	chr1:70820800-70821400	Flanking Active TSS	HepG2	liver
27	chr1:70820800-70821400	Flanking Active TSS	K562	blood
28	chr1:70821000-70821400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:70821000-70821400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:70821000-70821400	Enhancers	Primary B cells from cord blood	blood
31	chr1:70821000-70821400	Enhancers	Primary B cells from peripheral blood	blood
32	chr1:70821000-70821400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:70821000-70821400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:70821000-70821400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:70821000-70821400	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr1:70821000-70821400	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:70821000-70821400	Enhancers	Small Intestine	intestine
38	chr1:70821000-70822000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr1:70821000-70822400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr1:70821000-70824000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:70821000-70827600	Weak transcription	HSMM	muscle
42	chr1:70821000-70835200	Weak transcription	Pancreas	Pancrea
43	chr1:70821000-70836400	Weak transcription	Left Ventricle	heart
44	chr1:70821000-70838400	Weak transcription	Lung	lung
45	chr1:70821200-70821400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:70821200-70821400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr1:70821200-70821400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:70821200-70821400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr1:70821200-70821400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr1:70821200-70821400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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