Variant report

Variant	rs12742313
Chromosome Location	chr1:225653865-225653866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225652849..225654996-chr1:225964946..225967311,2	MCF-7	breast:
2	chr1:91487179..91487687-chr1:225653229..225653962,2	Hela-S3	cervix:
3	chr1:225616757..225618444-chr1:225653517..225655559,2	K562	blood:

Variant related genes	Relation type
ENSG00000143742	Chromatin interaction
ENSG00000122482	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10799312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915831	0.83[ASN][1000 genomes]
rs12032961	0.81[ASN][1000 genomes]
rs12124353	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1340865	0.80[ASN][1000 genomes]
rs2185528	0.83[ASN][1000 genomes]
rs3766930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3856157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3893032	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233220	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4554690	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6426075	0.81[ASN][1000 genomes]
rs6692054	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7536925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225642400-225655200	Weak transcription	Small Intestine	intestine
2	chr1:225642600-225655000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:225647000-225654600	Enhancers	Fetal Thymus	thymus
4	chr1:225647000-225654800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:225647400-225654800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr1:225648800-225654600	Weak transcription	HUVEC	blood vessel
7	chr1:225649000-225654600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:225649200-225654400	Weak transcription	Primary T cells from cord blood	blood
9	chr1:225649800-225654800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:225649800-225662600	Weak transcription	Pancreas	Pancrea
11	chr1:225650200-225654600	Weak transcription	Spleen	Spleen
12	chr1:225651200-225655200	Weak transcription	Right Ventricle	heart
13	chr1:225651400-225654600	Weak transcription	Lung	lung
14	chr1:225651400-225662400	Weak transcription	Fetal Brain Male	brain
15	chr1:225651600-225654400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:225651600-225655000	Weak transcription	Stomach Mucosa	stomach
17	chr1:225651600-225655200	Weak transcription	Fetal Intestine Small	intestine
18	chr1:225651800-225654800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:225652000-225654400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:225652000-225655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:225652200-225654000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:225652400-225654000	Enhancers	Fetal Stomach	stomach
23	chr1:225652400-225655000	Enhancers	Rectal Smooth Muscle	rectum
24	chr1:225652400-225655200	Weak transcription	NHLF	lung
25	chr1:225652600-225654000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr1:225652600-225654600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:225652600-225654800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr1:225652600-225655200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:225652800-225654600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:225652800-225654600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:225653000-225654000	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr1:225653000-225654600	Enhancers	Primary B cells from cord blood	blood
33	chr1:225653000-225654800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:225653000-225654800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:225653200-225654000	Flanking Active TSS	Hela-S3	cervix
36	chr1:225653200-225654600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr1:225653200-225654600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr1:225653200-225654600	Weak transcription	GM12878-XiMat	blood
39	chr1:225653200-225654800	Enhancers	Primary B cells from peripheral blood	blood
40	chr1:225653200-225654800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:225653200-225654800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:225653400-225654400	Enhancers	Dnd41	blood
43	chr1:225653400-225654600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:225653400-225654800	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr1:225653400-225654800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:225653400-225654800	Weak transcription	Osteobl	bone
47	chr1:225653400-225655000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:225653400-225655000	Weak transcription	Left Ventricle	heart
49	chr1:225653400-225655200	Weak transcription	Fetal Lung	lung
50	chr1:225653600-225654000	Bivalent Enhancer	Fetal Muscle Leg	muscle

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