Variant report

Variant	rs13103899
Chromosome Location	chr4:120438302-120438303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:120430071..120433986-chr4:120435294..120438761,4	K562	blood:
2	chr4:120431676..120434490-chr4:120437261..120440193,2	K562	blood:
3	chr4:120437151..120439080-chr4:120441248..120444121,2	K562	blood:

Variant related genes	Relation type
ENSG00000245958	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10012485	0.89[CEU][hapmap]
rs10025536	0.82[EUR][1000 genomes]
rs10518335	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs11724055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11730798	0.82[EUR][1000 genomes]
rs11731568	0.82[EUR][1000 genomes]
rs12108288	1.00[YRI][hapmap]
rs12646525	0.89[CEU][hapmap];0.94[TSI][hapmap]
rs13103510	0.84[EUR][1000 genomes]
rs13106925	0.82[EUR][1000 genomes]
rs13107334	1.00[ASW][hapmap];0.81[GIH][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13116789	1.00[CHB][hapmap]
rs13118388	0.82[EUR][1000 genomes]
rs13120581	0.82[EUR][1000 genomes]
rs13121569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13124532	0.87[TSI][hapmap]
rs13133969	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13136296	0.82[EUR][1000 genomes]
rs13137511	0.82[EUR][1000 genomes]
rs13140150	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17292047	1.00[CHB][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17358524	1.00[CHB][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs17358860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1987179	0.89[CEU][hapmap];0.94[TSI][hapmap]
rs2248236	0.89[CEU][hapmap]
rs2389863	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs2389866	0.89[CEU][hapmap]
rs2389868	0.82[EUR][1000 genomes]
rs2389869	0.89[CEU][hapmap];0.94[TSI][hapmap]
rs2389870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622499	0.89[CEU][hapmap];0.94[TSI][hapmap]
rs2953295	0.80[EUR][1000 genomes]
rs34601943	0.82[EUR][1000 genomes]
rs34676199	0.82[EUR][1000 genomes]
rs35264119	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35289699	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35850447	0.82[EUR][1000 genomes]
rs35967840	0.82[EUR][1000 genomes]
rs35999787	0.82[EUR][1000 genomes]
rs3756154	0.89[CEU][hapmap];0.94[TSI][hapmap]
rs3756155	0.82[EUR][1000 genomes]
rs3775846	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775851	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3775856	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4833620	0.82[EUR][1000 genomes]
rs4834782	0.83[EUR][1000 genomes]
rs4834788	0.82[EUR][1000 genomes]
rs4834789	0.82[EUR][1000 genomes]
rs4834790	0.81[EUR][1000 genomes]
rs61747388	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62319574	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62319578	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62319606	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62319609	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62319612	0.83[EUR][1000 genomes]
rs62319647	0.82[EUR][1000 genomes]
rs62319657	0.82[EUR][1000 genomes]
rs62319658	0.82[EUR][1000 genomes]
rs6817975	0.82[EUR][1000 genomes]
rs71614451	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7684899	0.88[CEU][hapmap]
rs988146	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879844	chr4:120341296-120449810	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv879846	chr4:120341296-120491714	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv879847	chr4:120371729-120450159	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	esv1802153	chr4:120397829-120457682	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh 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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13103899	RP11-33B1.1	cis	Thyroid	GTEx
rs13103899	USP53	cis	parietal	SCAN
rs13103899	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120376400-120471600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:120377400-120439000	Weak transcription	Small Intestine	intestine
3	chr4:120377400-120439000	Weak transcription	Spleen	Spleen
4	chr4:120377600-120441000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
6	chr4:120384400-120439200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:120397800-120442600	Weak transcription	Hela-S3	cervix
8	chr4:120403400-120445800	Weak transcription	A549	lung
9	chr4:120414400-120440400	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr4:120415200-120438800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:120417200-120439400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:120417600-120445800	Weak transcription	NHEK	skin
13	chr4:120419600-120439200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:120420200-120439000	Weak transcription	GM12878-XiMat	blood
15	chr4:120420200-120440200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:120420200-120440200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:120420200-120485400	Weak transcription	Fetal Brain Male	brain
18	chr4:120420400-120449600	Weak transcription	Brain Angular Gyrus	brain
19	chr4:120421000-120443600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:120421000-120445600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:120421200-120455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:120421400-120439000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:120421600-120439000	Weak transcription	HUVEC	blood vessel
24	chr4:120422000-120446400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:120422800-120446600	Weak transcription	Fetal Stomach	stomach
26	chr4:120422800-120448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:120423400-120450600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:120428000-120444800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr4:120430400-120439000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:120430800-120439400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:120430800-120447400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:120432400-120438600	Weak transcription	Fetal Heart	heart
33	chr4:120432400-120440600	Strong transcription	Primary B cells from cord blood	blood
34	chr4:120432400-120441200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:120432600-120439800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:120432800-120439400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:120432800-120443000	Strong transcription	Primary T cells from cord blood	blood
38	chr4:120433200-120439400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:120433400-120439400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr4:120433400-120441600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr4:120433400-120442600	Strong transcription	Fetal Thymus	thymus
42	chr4:120433400-120442800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:120433400-120442800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr4:120433400-120444600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr4:120433600-120439400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr4:120433600-120439600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr4:120433600-120440000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr4:120433600-120440400	Strong transcription	Dnd41	blood
49	chr4:120433600-120442200	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:120433600-120442800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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