Variant report

Variant	rs3750549
Chromosome Location	chr9:71831026-71831027
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71830973..71832633-chr9:71834177..71836449,2	K562	blood:
2	chr9:71806704..71808402-chr9:71829211..71831372,2	K562	blood:
3	chr9:71830973..71833151-chr9:71834177..71836449,3	K562	blood:
4	chr9:71830235..71832170-chr9:71836510..71838640,2	K562	blood:

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10125494	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs10217168	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs10735655	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10781440	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs10781456	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs10781479	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10869961	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs10869975	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs10869992	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10869993	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10869994	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10869997	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10870006	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10870012	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10870015	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10870017	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11145460	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs11145627	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11145648	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11145688	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12056979	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs1339546	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1416738	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1538584	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs17062237	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17062397	0.87[CHB][hapmap]
rs2309422	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2309424	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2309425	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2309426	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2309427	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486449	0.99[ASN][1000 genomes]
rs2486451	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2486452	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2498436	0.91[ASN][1000 genomes]
rs2993818	0.87[ASN][1000 genomes]
rs2993819	0.91[ASN][1000 genomes]
rs2993820	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3002377	0.91[ASN][1000 genomes]
rs3002378	0.91[ASN][1000 genomes]
rs3002379	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs3002380	0.91[ASN][1000 genomes]
rs3002382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3927676	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4076287	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4338173	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4375066	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4576478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4592105	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs4745646	0.87[CHB][hapmap]
rs4745701	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs55641500	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56226859	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56312702	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58264616	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60785288	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61074083	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62567148	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6560618	0.91[ASN][1000 genomes]
rs6560627	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020869	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7038854	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7041781	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043149	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs7045103	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7048648	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7350225	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7467352	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs7850766	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7861292	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7862404	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs7864775	0.91[ASN][1000 genomes]
rs7865373	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs7873004	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874888	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867346	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs884428	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs884429	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9410783	0.89[ASN][1000 genomes]
rs9411195	0.93[ASN][1000 genomes]
rs9411200	0.91[ASN][1000 genomes]
rs946540	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv466397	chr9:71574757-71843023	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv614550	chr9:71574757-71843023	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1050692	chr9:71578494-71843023	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv1040539	chr9:71600042-71844108	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv540149	chr9:71600042-71844108	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv949664	chr9:71607398-71842391	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
15	nsv948708	chr9:71632265-71842391	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
17	nsv893427	chr9:71762766-71858517	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3750549	TJP2	cis	Whole Blood	GTEx
rs3750549	TJP2	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71790400-71832200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:71790400-71835600	Weak transcription	Colonic Mucosa	Colon
3	chr9:71797200-71832000	Weak transcription	Esophagus	oesophagus
4	chr9:71804000-71831800	Weak transcription	Aorta	Aorta
5	chr9:71807400-71832200	Weak transcription	Primary T cells from cord blood	blood
6	chr9:71807800-71842800	Weak transcription	Small Intestine	intestine
7	chr9:71810400-71832400	Weak transcription	GM12878-XiMat	blood
8	chr9:71815200-71832200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:71816000-71831200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:71819800-71842200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:71820200-71831200	Weak transcription	NHEK	skin
12	chr9:71820200-71831800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:71820200-71831800	Weak transcription	Placenta	Placenta
14	chr9:71820200-71832000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:71820200-71832400	Weak transcription	HMEC	breast
16	chr9:71820200-71833000	Weak transcription	HSMM	muscle
17	chr9:71820200-71842200	Weak transcription	NH-A	brain
18	chr9:71820400-71832000	Weak transcription	Osteobl	bone
19	chr9:71820400-71833200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:71820400-71840400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:71820400-71842200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:71820800-71831200	Weak transcription	NHLF	lung
23	chr9:71820800-71831600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:71820800-71835800	Weak transcription	Psoas Muscle	Psoas
25	chr9:71820800-71840200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:71821400-71840200	Weak transcription	Brain Anterior Caudate	brain
27	chr9:71822800-71831800	Weak transcription	Lung	lung
28	chr9:71822800-71832000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:71822800-71836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:71823000-71832200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr9:71823000-71832200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:71823000-71835800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:71823400-71831400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr9:71825200-71832000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr9:71825400-71833600	Enhancers	Fetal Heart	heart
36	chr9:71825400-71834200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr9:71825800-71831600	Enhancers	Ovary	ovary
38	chr9:71826800-71834000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:71826800-71835600	Weak transcription	Right Ventricle	heart
40	chr9:71827000-71831600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr9:71827400-71831200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:71827400-71832200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr9:71827400-71833600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr9:71827400-71835800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr9:71827600-71832000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr9:71828000-71833000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:71828000-71840400	Strong transcription	Fetal Intestine Small	intestine
48	chr9:71828000-71866000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:71828200-71831200	Enhancers	Liver	Liver
50	chr9:71828400-71832000	Weak transcription	Left Ventricle	heart

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