Variant report

Variant	rs12491029
Chromosome Location	chr3:47509095-47509096
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1024036	0.93[YRI][hapmap]
rs10865947	1.00[YRI][hapmap]
rs11707272	1.00[YRI][hapmap]
rs13077134	1.00[YRI][hapmap]
rs1531874	1.00[YRI][hapmap]
rs1872165	1.00[YRI][hapmap]
rs2170814	1.00[YRI][hapmap]
rs295432	1.00[YRI][hapmap]
rs295434	1.00[YRI][hapmap]
rs295443	1.00[YRI][hapmap]
rs295448	1.00[YRI][hapmap]
rs295450	1.00[YRI][hapmap]
rs295451	1.00[YRI][hapmap]
rs295454	1.00[YRI][hapmap]
rs295456	1.00[YRI][hapmap]
rs295457	1.00[YRI][hapmap]
rs295459	1.00[YRI][hapmap]
rs4858812	1.00[YRI][hapmap]
rs4858823	1.00[YRI][hapmap]
rs6442068	1.00[YRI][hapmap]
rs6442069	1.00[YRI][hapmap]
rs6778673	1.00[YRI][hapmap]
rs7372780	1.00[YRI][hapmap]
rs7644043	1.00[YRI][hapmap]
rs807930	1.00[YRI][hapmap]
rs900689	0.93[YRI][hapmap]
rs900690	1.00[YRI][hapmap]
rs900693	0.86[YRI][hapmap]
rs900694	1.00[YRI][hapmap]
rs903538	1.00[YRI][hapmap]
rs924009	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv3806	chr3:47488784-47518133	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv1816532	chr3:47490712-47511698	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv1841538	chr3:47490712-47511698	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1848062	chr3:47490712-47511698	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1849930	chr3:47490712-47511698	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47476600-47514200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:47484000-47511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:47484200-47511200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr3:47484600-47514000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:47484600-47514200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr3:47484600-47514200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:47484600-47514200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:47484600-47514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:47484800-47514800	Weak transcription	Thymus	Thymus
10	chr3:47485000-47514800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:47486000-47516000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:47486000-47516000	Weak transcription	Small Intestine	intestine
13	chr3:47486000-47516000	Weak transcription	HSMM	muscle
14	chr3:47486200-47516000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:47493400-47510800	Weak transcription	Spleen	Spleen
16	chr3:47494600-47514000	Weak transcription	Esophagus	oesophagus
17	chr3:47494600-47514000	Weak transcription	Pancreas	Pancrea
18	chr3:47494800-47511200	Weak transcription	Psoas Muscle	Psoas
19	chr3:47495400-47514600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:47497600-47511400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:47497800-47511400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:47497800-47514800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:47497800-47514800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:47497800-47514800	Weak transcription	Hela-S3	cervix
25	chr3:47497800-47516000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:47497800-47516000	Weak transcription	A549	lung
27	chr3:47497800-47516000	Weak transcription	NHDF-Ad	bronchial
28	chr3:47498000-47511000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:47498800-47510600	Weak transcription	Fetal Brain Female	brain
30	chr3:47498800-47516000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:47499000-47511600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:47499200-47514200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:47501000-47516200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:47501400-47516200	Weak transcription	HSMMtube	muscle
35	chr3:47502400-47516000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:47502800-47510600	Weak transcription	Fetal Intestine Large	intestine
37	chr3:47502800-47514800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:47502800-47515400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:47503200-47516000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:47503400-47516000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:47504000-47516200	Weak transcription	Gastric	stomach
42	chr3:47504400-47514000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:47504800-47510600	Weak transcription	Fetal Thymus	thymus
44	chr3:47504800-47514600	Weak transcription	Primary T cells from cord blood	blood
45	chr3:47504800-47514800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:47504800-47514800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:47504800-47515000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:47505000-47510600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:47505000-47511200	Weak transcription	K562	blood
50	chr3:47505000-47514600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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