Variant report

Variant	rs3797983
Chromosome Location	chr5:9336932-9336933
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:9335941..9338065-chr5:9339507..9341080,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10462867	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1205715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1205724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12655979	1.00[CEU][hapmap]
rs12658330	1.00[CEU][hapmap]
rs13355242	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[EUR][1000 genomes]
rs16882400	1.00[EUR][1000 genomes]
rs16882463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16882519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1806015	1.00[CEU][hapmap]
rs3734150	1.00[CEU][hapmap]
rs3777323	1.00[CEU][hapmap]
rs3797993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3797997	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3797999	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3798000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41482053	1.00[CEU][hapmap]
rs60031337	1.00[EUR][1000 genomes]
rs73742654	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7702342	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1020815	chr5:9135207-9425649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv498044	chr5:9143754-9402870	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv530183	chr5:9146506-9413373	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3797983	SEMA5A	cis	lymphoblastoid	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9308800-9346600	Weak transcription	Ovary	ovary
2	chr5:9329400-9337800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:9331200-9346000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:9331600-9338000	Weak transcription	NH-A	brain
5	chr5:9332000-9339200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:9332600-9349000	Weak transcription	Right Ventricle	heart
7	chr5:9332800-9337000	Weak transcription	NHLF	lung
8	chr5:9332800-9338000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:9332800-9338000	Weak transcription	Fetal Kidney	kidney
10	chr5:9332800-9341000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:9332800-9342400	Weak transcription	Pancreas	Pancrea
12	chr5:9332800-9346200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:9332800-9346200	Weak transcription	Fetal Intestine Small	intestine
14	chr5:9332800-9346600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr5:9332800-9348000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:9332800-9372400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:9333000-9346400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:9334800-9337000	Weak transcription	Fetal Heart	heart
19	chr5:9334800-9337400	Weak transcription	Brain Anterior Caudate	brain
20	chr5:9335000-9337200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:9335200-9338000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:9335200-9345000	Weak transcription	Left Ventricle	heart
23	chr5:9335400-9338400	Enhancers	NHDF-Ad	bronchial
24	chr5:9335600-9337000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr5:9335600-9337000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:9335600-9337000	Strong transcription	Liver	Liver
27	chr5:9335600-9337000	Enhancers	HMEC	breast
28	chr5:9335800-9337200	Strong transcription	Fetal Intestine Large	intestine
29	chr5:9335800-9346200	Weak transcription	Fetal Stomach	stomach
30	chr5:9336000-9337800	Weak transcription	Fetal Muscle Leg	muscle
31	chr5:9336200-9337000	Strong transcription	Fetal Lung	lung
32	chr5:9336200-9341000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:9336400-9337000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:9336400-9338000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:9336600-9337200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:9336600-9337400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:9336600-9337600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:9336600-9337800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:9336600-9338000	Weak transcription	Osteobl	bone
40	chr5:9336800-9337400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:9336800-9337400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:9336800-9337800	Weak transcription	NHEK	skin
43	chr5:9336800-9338000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:9336800-9338000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:9336800-9342600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:9336800-9343800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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