Variant report

Variant	rs12405164
Chromosome Location	chr1:226837016-226837017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226836884..226839158-chr1:226845149..226848067,3	K562	blood:
2	chr1:226834690..226837543-chr1:226839422..226842104,4	K562	blood:
3	chr1:226832724..226834932-chr1:226836674..226839333,2	MCF-7	breast:
4	chr1:226836459..226838161-chr1:226889738..226891302,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228382	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12077348	0.81[EUR][1000 genomes]
rs12568026	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236604	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35483910	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754387	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3768371	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3768372	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768373	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3820636	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv873235	chr1:226819073-226851963	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3437235	chr1:226835029-226839227	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226814200-226837600	Weak transcription	HUVEC	blood vessel
2	chr1:226814800-226840600	Weak transcription	Small Intestine	intestine
3	chr1:226820400-226840800	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr1:226823200-226841400	Weak transcription	NHDF-Ad	bronchial
5	chr1:226823800-226837400	Strong transcription	Dnd41	blood
6	chr1:226828000-226837200	Genic enhancers	Brain Hippocampus Middle	brain
7	chr1:226829400-226843800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:226830400-226840400	Genic enhancers	Primary T cells from cord blood	blood
9	chr1:226830400-226840400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr1:226830600-226838000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:226831200-226837400	Genic enhancers	Brain Substantia Nigra	brain
12	chr1:226831400-226841600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:226832000-226838400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:226832000-226843800	Weak transcription	HMEC	breast
15	chr1:226832200-226837200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:226832200-226837400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:226832400-226837400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:226832400-226843600	Weak transcription	Stomach Mucosa	stomach
19	chr1:226832800-226837400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:226832800-226837400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:226833000-226837200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr1:226833000-226838800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
23	chr1:226833400-226837200	Strong transcription	GM12878-XiMat	blood
24	chr1:226833400-226837400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:226833400-226837400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:226833600-226844000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:226833800-226837400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:226833800-226838200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:226833800-226841600	Weak transcription	Fetal Heart	heart
30	chr1:226834000-226837400	Weak transcription	Right Atrium	heart
31	chr1:226834200-226838200	Strong transcription	Thymus	Thymus
32	chr1:226834400-226837200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:226834400-226837600	Strong transcription	Fetal Stomach	stomach
34	chr1:226834400-226838600	Weak transcription	Psoas Muscle	Psoas
35	chr1:226834600-226837200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:226834600-226841400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:226834800-226837200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:226834800-226837400	Strong transcription	Primary B cells from cord blood	blood
39	chr1:226834800-226837400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:226834800-226837600	Strong transcription	Fetal Thymus	thymus
41	chr1:226835000-226837200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:226835000-226837200	Strong transcription	Spleen	Spleen
43	chr1:226835200-226837400	Strong transcription	NHEK	skin
44	chr1:226835200-226841600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:226835400-226837200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:226835600-226838000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:226835600-226838000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:226835600-226838400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:226835800-226837800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:226835800-226837800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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