Variant report

Variant	rs28397987
Chromosome Location	chr14:35619614-35619615
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	chr14:35617849..35620759-chr14:35622945..35624771,2	K562	blood:
2	chr14:35618961..35620951-chr14:35872636..35874969,2	K562	blood:

Variant related genes	Relation type
ENSG00000100906	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1056879	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11156875	0.82[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11851907	0.90[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17103005	0.86[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17103034	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1807161	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1961195	0.88[ASN][1000 genomes]
rs2010648	0.82[ASN][1000 genomes]
rs2143950	0.80[JPT][hapmap]
rs2179890	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs2236167	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28399702	0.83[ASN][1000 genomes]
rs28765972	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2899830	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3809449	0.82[CHD][hapmap]
rs4594164	0.82[CHD][hapmap]
rs55977244	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56027918	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57473972	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7142489	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs7146682	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153660	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158416	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7158634	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7159324	0.82[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs72664807	0.87[ASN][1000 genomes]
rs8005406	0.82[ASN][1000 genomes]
rs8006884	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8014091	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8014377	0.82[CHD][hapmap]
rs8019351	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9671773	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv1043470	chr14:35398522-35754029	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats 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	65 gene(s)	inside rSNPs	diseases
3	nsv542031	chr14:35398522-35754029	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	65 gene(s)	inside rSNPs	diseases
4	nsv564264	chr14:35482797-35732369	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv901615	chr14:35485748-35630175	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1044515	chr14:35510785-35756317	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS 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	42 gene(s)	inside rSNPs	diseases
8	nsv564265	chr14:35512335-35624831	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats 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	38 gene(s)	inside rSNPs	diseases
9	nsv1046992	chr14:35527239-35724227	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
10	nsv1051274	chr14:35529529-35724227	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv1048823	chr14:35537281-35724892	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
12	nsv542032	chr14:35537281-35724892	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv1040540	chr14:35537481-35724753	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv542033	chr14:35537481-35724753	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv1042625	chr14:35546094-35680358	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
16	nsv1050123	chr14:35546114-35724892	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers 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	27 gene(s)	inside rSNPs	diseases
17	nsv542034	chr14:35546114-35724892	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
18	nsv1050700	chr14:35548276-35639084	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS 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	21 gene(s)	inside rSNPs	diseases
19	nsv1043692	chr14:35548276-35720016	Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv1053604	chr14:35548276-35825805	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
21	nsv1047992	chr14:35563220-35639084	Enhancers Weak transcription Strong transcription Active TSS Flanking 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	21 gene(s)	inside rSNPs	diseases
22	nsv1052392	chr14:35563220-35893309	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
23	nsv542036	chr14:35563220-35893309	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
24	nsv1053978	chr14:35571762-35639084	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
25	nsv534182	chr14:35579022-35620232	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
26	nsv1240	chr14:35599027-35625361	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
27	nsv1040300	chr14:35602956-35643888	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
28	nsv1046680	chr14:35608347-35665374	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28397987	PPP2R3C	cis	Whole Blood	GTEx
rs28397987	PPP2R3C	cis	lymphoblastoid	seeQTL
rs28397987	PPP2R3C	cis	parietal	SCAN
rs28397987	PPP2R3C	cis	multi-tissue	Pritchard
rs28397987	PPP2R3C	Cis_1M	lymphoblastoid	RTeQTL
rs28397987	FAM177A1	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35592600-35625200	Weak transcription	Small Intestine	intestine
2	chr14:35593000-35638200	Weak transcription	Fetal Brain Male	brain
3	chr14:35593000-35660400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr14:35593200-35625200	Weak transcription	NH-A	brain
5	chr14:35593200-35625600	Weak transcription	Colon Smooth Muscle	Colon
6	chr14:35593200-35627800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr14:35593200-35635400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr14:35594400-35629000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr14:35596000-35623600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr14:35597400-35625000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr14:35597600-35625000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr14:35603000-35625200	Weak transcription	HSMM	muscle
13	chr14:35603200-35623200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr14:35603200-35663400	Weak transcription	Fetal Lung	lung
15	chr14:35603400-35625200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr14:35603600-35621600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr14:35604000-35624400	Weak transcription	NHEK	skin
18	chr14:35604200-35623200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr14:35604200-35625200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr14:35604200-35625200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr14:35604200-35628800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr14:35604200-35651400	Weak transcription	Esophagus	oesophagus
23	chr14:35604400-35621800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr14:35604400-35623200	Weak transcription	A549	lung
25	chr14:35604400-35625200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr14:35604400-35625200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr14:35604400-35642000	Weak transcription	Lung	lung
28	chr14:35604400-35651800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr14:35604400-35660200	Weak transcription	Aorta	Aorta
30	chr14:35604600-35620600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr14:35604600-35625200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr14:35604600-35625200	Weak transcription	Adipose Nuclei	Adipose
33	chr14:35604600-35626000	Weak transcription	Placenta	Placenta
34	chr14:35604600-35667400	Weak transcription	Spleen	Spleen
35	chr14:35604800-35624000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr14:35604800-35624600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr14:35604800-35625000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr14:35604800-35625200	Weak transcription	Liver	Liver
39	chr14:35604800-35625400	Weak transcription	HSMMtube	muscle
40	chr14:35605000-35625000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr14:35605600-35619800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr14:35605600-35625200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr14:35605600-35625200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr14:35605600-35625200	Weak transcription	Hela-S3	cervix
45	chr14:35605600-35628000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr14:35606400-35625200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr14:35607400-35628200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr14:35607400-35642800	Weak transcription	Left Ventricle	heart
49	chr14:35607400-35662000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr14:35607600-35624600	Weak transcription	HMEC	breast

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