Variant report

Variant	rs268531
Chromosome Location	chr5:9442192-9442193
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs268523	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs268525	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[EUR][1000 genomes]
rs268527	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs268530	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs452875	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs623033	1.00[CEU][hapmap];0.87[GIH][hapmap];0.87[LWK][hapmap];0.90[EUR][1000 genomes]
rs907655	1.00[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs268531	CHAD	trans	brain	seeQTL
rs268531	MTNR1A	trans	brain	seeQTL
rs268531	TMEM52	trans	brain	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9395800-9450200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:9432600-9444600	Weak transcription	Fetal Kidney	kidney
3	chr5:9433000-9444400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:9437400-9442400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:9437400-9446200	Weak transcription	Fetal Intestine Large	intestine
6	chr5:9437400-9477800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:9437800-9442200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:9437800-9442600	Enhancers	NHDF-Ad	bronchial
9	chr5:9438200-9442200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:9438600-9442600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:9438800-9442200	Enhancers	HMEC	breast
12	chr5:9438800-9442200	Enhancers	NHEK	skin
13	chr5:9438800-9442400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:9439000-9442200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:9439000-9442200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:9439000-9442400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:9439000-9444200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr5:9440400-9444400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:9440400-9448600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:9440400-9449200	Weak transcription	Fetal Lung	lung
21	chr5:9441000-9442200	Weak transcription	Fetal Stomach	stomach
22	chr5:9441200-9442600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:9441200-9442600	Enhancers	Placenta Amnion	Placenta Amnion
24	chr5:9441200-9443000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:9441200-9444400	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:9441200-9446400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr5:9441400-9442200	Weak transcription	NH-A	brain
28	chr5:9441400-9444200	Weak transcription	NHLF	lung
29	chr5:9441400-9446000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:9441400-9446200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:9441600-9442200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:9441600-9443200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:9441600-9443400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:9441600-9444200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:9441600-9456200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:9441800-9442200	Enhancers	Esophagus	oesophagus
37	chr5:9441800-9442200	Enhancers	Left Ventricle	heart
38	chr5:9441800-9442400	Enhancers	Right Ventricle	heart
39	chr5:9441800-9444000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:9442000-9445800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr5:9442000-9445800	Weak transcription	Fetal Heart	heart
42	chr5:9442000-9454000	Weak transcription	Osteobl	bone

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