Variant report

Variant	rs11938181
Chromosome Location	chr4:128839380-128839381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:128838666..128841299-chr4:128880030..128882225,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PGRMC2-3	chr4:128839307-128839542	NONHSAT098250

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11931314	1.00[ASW][hapmap]
rs11931833	0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11932251	1.00[AMR][1000 genomes]
rs11933103	1.00[AMR][1000 genomes]
rs11934357	0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11935267	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11941287	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11941857	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11942042	1.00[ASW][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11943141	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11943527	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11947194	0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11947313	1.00[ASW][hapmap];0.84[LWK][hapmap]
rs17012665	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];0.91[AFR][1000 genomes]
rs17012675	1.00[ASW][hapmap];0.84[LWK][hapmap];0.91[AFR][1000 genomes]
rs17012679	1.00[ASW][hapmap];0.84[LWK][hapmap];0.85[AFR][1000 genomes]
rs17012845	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[AMR][1000 genomes]
rs17012926	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs6534649	1.00[TSI][hapmap]
rs6534652	1.00[AMR][1000 genomes]
rs6820138	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1801492	chr4:128566686-128934513	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	esv1793579	chr4:128577439-128871309	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv3431515	chr4:128657260-128932577	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv532740	chr4:128710011-129035335	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv3416036	chr4:128782694-129133956	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv1033701	chr4:128803159-129095018	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv1019193	chr4:128810527-128949320	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	esv1841203	chr4:128817558-129043809	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
16	nsv1029890	chr4:128828468-129041302	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers 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	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128803400-128841800	Weak transcription	Brain Germinal Matrix	brain
2	chr4:128815400-128839400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr4:128817400-128839800	Weak transcription	HSMM	muscle
4	chr4:128817400-128841600	Weak transcription	Thymus	Thymus
5	chr4:128817400-128849400	Weak transcription	Osteobl	bone
6	chr4:128818800-128863000	Weak transcription	A549	lung
7	chr4:128821000-128841600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:128826600-128841600	Weak transcription	K562	blood
9	chr4:128831000-128841600	Weak transcription	HepG2	liver
10	chr4:128831200-128884600	Weak transcription	Spleen	Spleen
11	chr4:128832000-128841600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:128832600-128885200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:128832800-128841600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:128833000-128841000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr4:128833400-128858000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:128833600-128867600	Weak transcription	NHLF	lung
17	chr4:128833800-128841600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:128833800-128843800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:128834200-128841600	Weak transcription	Fetal Intestine Small	intestine
20	chr4:128834800-128839800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:128835000-128841400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:128835000-128885200	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:128835200-128841600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:128835200-128841800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:128835600-128841400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:128835800-128841600	Weak transcription	Colonic Mucosa	Colon
27	chr4:128836000-128864000	Weak transcription	Small Intestine	intestine
28	chr4:128836200-128840000	Weak transcription	Fetal Lung	lung
29	chr4:128836200-128840000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:128836200-128841400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:128836200-128841600	Weak transcription	Fetal Brain Female	brain
32	chr4:128836200-128847000	Weak transcription	Lung	lung
33	chr4:128836200-128847200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:128836400-128840000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:128836400-128840000	Weak transcription	Liver	Liver
36	chr4:128836400-128843800	Weak transcription	Stomach Mucosa	stomach
37	chr4:128836400-128850600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:128836400-128863000	Weak transcription	Fetal Kidney	kidney
39	chr4:128836600-128840800	Weak transcription	GM12878-XiMat	blood
40	chr4:128836600-128841600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr4:128836800-128841400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:128836800-128845000	Weak transcription	HUVEC	blood vessel
43	chr4:128836800-128884600	Weak transcription	Esophagus	oesophagus
44	chr4:128836800-128885200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:128837000-128868600	Weak transcription	Pancreas	Pancrea
46	chr4:128837000-128885800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr4:128837200-128841400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr4:128837200-128841600	Weak transcription	Brain Anterior Caudate	brain
49	chr4:128837200-128842600	Weak transcription	NHEK	skin
50	chr4:128837400-128840400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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