Variant report

Variant	rs792440
Chromosome Location	chr1:212528568-212528569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:212528417-212528973	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:212528456-212529208	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr1:212528479-212529090	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212526274..212530393-chr1:212532499..212537435,6	K562	blood:
2	chr1:212519088..212521774-chr1:212528493..212530419,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229832	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12725070	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444692	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1774252	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2921127	0.87[ASN][1000 genomes]
rs2921128	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2921129	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2995255	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2995256	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2995257	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2995258	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3099111	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3121291	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351383	0.89[ASN][1000 genomes]
rs351392	1.00[YRI][hapmap]
rs351395	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs351397	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs351416	1.00[YRI][hapmap]
rs4554777	1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6674587	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs701906	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs701907	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs701908	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs792433	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792434	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs792441	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs792442	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs792443	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs812074	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[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	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212489600-212554800	Weak transcription	Small Intestine	intestine
2	chr1:212493800-212533400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:212500000-212540400	Weak transcription	Stomach Mucosa	stomach
4	chr1:212501000-212533600	Weak transcription	Fetal Heart	heart
5	chr1:212501400-212540800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:212501800-212540800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:212502800-212541400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:212504000-212548600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:212504400-212537600	Weak transcription	Psoas Muscle	Psoas
12	chr1:212505200-212531400	Weak transcription	HMEC	breast
13	chr1:212505800-212533200	Weak transcription	NH-A	brain
14	chr1:212508200-212545800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:212508600-212541000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:212511400-212540800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr1:212513200-212541000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:212513800-212540800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:212514400-212540400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:212514600-212537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:212514800-212541800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:212515000-212528600	Strong transcription	Dnd41	blood
23	chr1:212515200-212536400	Strong transcription	Liver	Liver
24	chr1:212515400-212528600	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr1:212516000-212528600	Strong transcription	Adipose Nuclei	Adipose
26	chr1:212518400-212531200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:212522600-212529600	Weak transcription	NHDF-Ad	bronchial
28	chr1:212523600-212550600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:212524000-212541800	Strong transcription	Fetal Thymus	thymus
30	chr1:212524400-212528600	Strong transcription	GM12878-XiMat	blood
31	chr1:212524400-212554600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:212524600-212530800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:212525000-212541600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:212525400-212528600	Strong transcription	Left Ventricle	heart
35	chr1:212525400-212536600	Strong transcription	Primary B cells from cord blood	blood
36	chr1:212525600-212528600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:212525600-212528600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:212525600-212528600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr1:212525600-212541800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:212525600-212545600	Strong transcription	Primary T cells from cord blood	blood
41	chr1:212526400-212531400	Weak transcription	NHEK	skin
42	chr1:212526600-212529600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:212526600-212530000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:212526600-212530200	Weak transcription	Hela-S3	cervix
45	chr1:212526600-212532600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:212526600-212535000	Weak transcription	Fetal Brain Female	brain
47	chr1:212526600-212540600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:212526600-212540800	Weak transcription	Right Ventricle	heart
49	chr1:212526800-212529400	Weak transcription	HUVEC	blood vessel
50	chr1:212526800-212529600	Weak transcription	Brain Anterior Caudate	brain

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