Variant report

Variant	rs7681051
Chromosome Location	chr4:151314440-151314441
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12499470	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500337	0.89[ASN][1000 genomes]
rs12502486	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503093	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12506612	0.82[ASN][1000 genomes]
rs12507785	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12508149	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17504359	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17504442	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17589028	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17589134	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1979920	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2036552	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2360071	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41386148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56714695	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535735	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6812262	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6817796	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6833359	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6839345	0.82[ASN][1000 genomes]
rs6849869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7677055	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7699001	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180280	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs952097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv880259	chr4:151210761-151367745	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv880260	chr4:151214038-151331191	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv830112	chr4:151243801-151431771	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv527113	chr4:151314315-151316434	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7681051	TTC29	cis	cerebellum	SCAN
rs7681051	LRBA	cis	parietal	SCAN
rs7681051	PLRG1	cis	parietal	SCAN
rs7681051	FAM160A1	cis	parietal	SCAN
rs7681051	LRBA	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151272000-151371400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:151286600-151355600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr4:151290200-151367400	Weak transcription	K562	blood
4	chr4:151292400-151361000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:151296000-151317200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:151299800-151314600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:151301600-151315600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:151307000-151348800	Weak transcription	Aorta	Aorta
9	chr4:151307200-151315000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:151307200-151323400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:151307200-151324000	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:151307200-151324200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:151307200-151332400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:151307400-151314600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:151309600-151314600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:151309600-151332600	Weak transcription	Stomach Mucosa	stomach
17	chr4:151311200-151314600	Strong transcription	Primary T cells from cord blood	blood
18	chr4:151311600-151343800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:151312600-151314600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:151312800-151332400	Weak transcription	Primary B cells from cord blood	blood
21	chr4:151313000-151316600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:151313200-151358200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr4:151313600-151358000	Weak transcription	GM12878-XiMat	blood
24	chr4:151314000-151314800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:151314000-151315400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:151314000-151324200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:151314200-151315600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
28	chr4:151314200-151324200	Weak transcription	Pancreas	Pancrea
29	chr4:151314400-151315000	ZNF genes & repeats	Fetal Intestine Large	intestine

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