Variant report

Variant	rs7423942
Chromosome Location	chr2:96645257-96645258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11683523	0.83[CEU][hapmap]
rs11687113	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs11689832	0.84[CEU][hapmap]
rs12623771	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2438924	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2438972	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs2438978	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs2579518	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2579519	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2918816	0.81[EUR][1000 genomes]
rs4144055	0.84[EUR][1000 genomes]
rs4527246	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4907226	0.87[EUR][1000 genomes]
rs4907288	0.92[CEU][hapmap]
rs62155510	0.88[EUR][1000 genomes]
rs6740563	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs72492201	0.82[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	esv14492	chr2:96591462-96647854	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7423942	FAHD2CP	cis	lung	GTEx
rs7423942	GPAT2	cis	Nerve Tibial	GTEx
rs7423942	ADRA2B	cis	Thyroid	GTEx

Chromatin state (count:71 , 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	chr2:96577800-96647800	Weak transcription	NHDF-Ad	bronchial
3	chr2:96577800-96651000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:96577800-96656600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:96582800-96656400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:96585200-96649000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:96586000-96657200	Weak transcription	Ovary	ovary
8	chr2:96587800-96656600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:96588200-96649000	Weak transcription	Fetal Intestine Large	intestine
10	chr2:96589000-96645400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:96600600-96657200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:96605600-96655000	Weak transcription	HUVEC	blood vessel
13	chr2:96606400-96657200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:96607400-96657200	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:96611000-96656600	Weak transcription	Osteobl	bone
16	chr2:96611400-96657200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr2:96614400-96655800	Weak transcription	K562	blood
18	chr2:96615200-96650000	Weak transcription	Brain Substantia Nigra	brain
19	chr2:96616600-96645400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:96616800-96657200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:96617000-96656600	Weak transcription	Fetal Stomach	stomach
22	chr2:96617000-96656800	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:96617200-96656800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:96617800-96656600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:96618200-96648000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:96620600-96645400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:96621800-96657200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:96623000-96648800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:96624000-96658200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:96624400-96656600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:96625200-96656600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:96626200-96656600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:96628000-96657200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:96628200-96646200	Weak transcription	Fetal Brain Female	brain
35	chr2:96628200-96656400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:96628200-96657200	Weak transcription	Left Ventricle	heart
37	chr2:96628600-96647600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr2:96640800-96648200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:96641600-96657200	Weak transcription	Fetal Heart	heart
40	chr2:96642200-96645800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:96643000-96656400	Weak transcription	HMEC	breast
42	chr2:96643200-96646600	Strong transcription	Dnd41	blood
43	chr2:96644000-96648200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:96644000-96656400	Weak transcription	Brain Germinal Matrix	brain
45	chr2:96644000-96656800	Weak transcription	Right Ventricle	heart
46	chr2:96644200-96645800	Strong transcription	Fetal Thymus	thymus
47	chr2:96644200-96646600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:96644200-96656600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:96644600-96645400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:96644600-96645600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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