Variant report

Variant	rs4144055
Chromosome Location	chr2:96647856-96647857
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11680950	0.82[GIH][hapmap];0.88[YRI][hapmap]
rs11683523	0.89[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs11687113	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1168965	0.88[GIH][hapmap];0.83[LWK][hapmap]
rs1168968	0.91[GIH][hapmap];0.82[LWK][hapmap]
rs1168974	0.91[GIH][hapmap];0.88[YRI][hapmap]
rs1168975	0.88[YRI][hapmap]
rs1168976	0.91[GIH][hapmap];0.88[YRI][hapmap]
rs11689832	0.95[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs11695514	0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs2312955	0.91[GIH][hapmap];0.83[LWK][hapmap]
rs2438978	0.81[CEU][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs2462774	1.00[YRI][hapmap]
rs2579515	0.85[ASN][1000 genomes]
rs2579517	0.85[ASN][1000 genomes]
rs2579519	0.89[GIH][hapmap]
rs2692893	0.89[CHD][hapmap];0.97[GIH][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap]
rs2692894	0.91[GIH][hapmap]
rs2692954	0.85[ASN][1000 genomes]
rs2918816	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2969475	0.85[ASN][1000 genomes]
rs2969477	0.86[ASN][1000 genomes]
rs4426564	0.91[GIH][hapmap];0.83[LWK][hapmap]
rs4613328	0.86[AFR][1000 genomes]
rs4907226	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4907288	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs62155508	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62155510	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62155511	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6740563	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72492201	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7423942	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv874660	chr2:96091132-96669134	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv516044	chr2:96150959-96683378	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1003371	chr2:96326106-96684876	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv874666	chr2:96370571-96691125	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv961832	chr2:96453677-96671971	Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv834304	chr2:96493545-96667472	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1004486	chr2:96544604-96684876	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv874669	chr2:96547820-96691125	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv818073	chr2:96554851-96683378	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
12	nsv870250	chr2:96610946-96739308	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	esv1838669	chr2:96613136-96674509	Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	esv1839005	chr2:96613136-96674509	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	esv1836246	chr2:96622689-96674509	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	esv1837811	chr2:96622689-96730375	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv874670	chr2:96637870-96693357	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	nsv874671	chr2:96637870-96727850	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv874672	chr2:96637870-96809331	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
20	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4144055	GPAT2	cis	Adipose Subcutaneous	GTEx
rs4144055	FAHD2CP	cis	lung	GTEx
rs4144055	ADRA2B	cis	Thyroid	GTEx
rs4144055	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs4144055	AC008268.2	cis	Nerve Tibial	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96557400-96656800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:96577800-96651000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:96577800-96656600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:96582800-96656400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:96585200-96649000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:96586000-96657200	Weak transcription	Ovary	ovary
7	chr2:96587800-96656600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:96588200-96649000	Weak transcription	Fetal Intestine Large	intestine
9	chr2:96600600-96657200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:96605600-96655000	Weak transcription	HUVEC	blood vessel
11	chr2:96606400-96657200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:96607400-96657200	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:96611000-96656600	Weak transcription	Osteobl	bone
14	chr2:96611400-96657200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:96614400-96655800	Weak transcription	K562	blood
16	chr2:96615200-96650000	Weak transcription	Brain Substantia Nigra	brain
17	chr2:96616800-96657200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:96617000-96656600	Weak transcription	Fetal Stomach	stomach
19	chr2:96617000-96656800	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:96617200-96656800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:96617800-96656600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:96618200-96648000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:96621800-96657200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:96623000-96648800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:96624000-96658200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:96624400-96656600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:96625200-96656600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:96626200-96656600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:96628000-96657200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:96628200-96656400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:96628200-96657200	Weak transcription	Left Ventricle	heart
32	chr2:96640800-96648200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:96641600-96657200	Weak transcription	Fetal Heart	heart
34	chr2:96643000-96656400	Weak transcription	HMEC	breast
35	chr2:96644000-96648200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:96644000-96656400	Weak transcription	Brain Germinal Matrix	brain
37	chr2:96644000-96656800	Weak transcription	Right Ventricle	heart
38	chr2:96644200-96656600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:96644800-96657200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:96645000-96648200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:96645400-96656600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:96645600-96655600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:96645600-96656400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:96645600-96656800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:96645800-96650600	Weak transcription	Fetal Thymus	thymus
46	chr2:96645800-96650800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:96645800-96656400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:96645800-96657200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:96645800-96657200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:96646000-96656400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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