Variant report

Variant	rs12616452
Chromosome Location	chr2:179971789-179971790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179966762..179969783-chr2:179969877..179973075,3	K562	blood:
2	chr2:179967469..179969783-chr2:179970648..179973075,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10173853	1.00[AMR][1000 genomes]
rs10176828	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10178559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10186707	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10205588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10207754	1.00[AMR][1000 genomes]
rs10208882	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10209875	1.00[CHB][hapmap]
rs10210749	0.85[ASN][1000 genomes]
rs10221811	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12328593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12329222	0.81[AFR][1000 genomes]
rs12611473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12612427	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12613089	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12617364	1.00[AMR][1000 genomes]
rs12622434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13382573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13383806	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13391187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13394908	1.00[AMR][1000 genomes]
rs13395559	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13408774	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13412820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13417112	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13422693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13424092	1.00[CHB][hapmap]
rs13429191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16866630	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16866647	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28508327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35041512	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734127	1.00[AMR][1000 genomes]
rs7578417	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7581898	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7588135	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7601965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7608106	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9288024	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179961600-179972400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:179961600-179972800	Weak transcription	Spleen	Spleen
3	chr2:179961600-179974000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:179961800-179972600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:179962000-179972600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:179962000-179972800	Weak transcription	Fetal Thymus	thymus
7	chr2:179962400-179972600	Weak transcription	Left Ventricle	heart
8	chr2:179962800-179972400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr2:179966200-179973000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:179966400-179972400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:179966400-179972600	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:179966400-179975600	Weak transcription	Aorta	Aorta
13	chr2:179966600-179972400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:179967000-179972200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:179967200-179976800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:179967400-179971800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:179967800-179980200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:179967800-179982400	Weak transcription	Fetal Brain Male	brain
19	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
20	chr2:179969000-179972400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:179969200-179972000	Enhancers	Rectal Smooth Muscle	rectum
22	chr2:179969200-179972800	Enhancers	Colon Smooth Muscle	Colon
23	chr2:179969200-179973000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:179969400-179972400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:179969400-179980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:179969600-179973000	Enhancers	HMEC	breast
27	chr2:179969800-179972600	Enhancers	Brain Substantia Nigra	brain
28	chr2:179970000-179972800	Weak transcription	Placenta	Placenta
29	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:179970200-179972000	Enhancers	Brain Anterior Caudate	brain
31	chr2:179970200-179972600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
33	chr2:179970400-179972800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:179970400-179977000	Weak transcription	Lung	lung
35	chr2:179970600-179972600	Enhancers	NHEK	skin
36	chr2:179970600-179973800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:179970800-179971800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:179970800-179972000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:179970800-179972200	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr2:179970800-179972400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:179970800-179972400	Weak transcription	Liver	Liver
42	chr2:179970800-179972400	Enhancers	Osteobl	bone
43	chr2:179970800-179973000	Enhancers	HSMMtube	muscle
44	chr2:179970800-179973200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:179970800-179973200	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr2:179970800-179973200	Enhancers	Fetal Intestine Small	intestine
47	chr2:179970800-179973200	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr2:179970800-179973400	Enhancers	HUVEC	blood vessel
49	chr2:179970800-179985800	Strong transcription	Primary B cells from cord blood	blood
50	chr2:179970800-179987000	Strong transcription	Monocytes-CD14+_RO01746	blood

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