Variant report

Variant	rs10135277
Chromosome Location	chr14:35823231-35823232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:35821416..35824471-chr14:35826109..35828501,4	K562	blood:
2	chr14:35821416..35823849-chr14:35826359..35828501,2	K562	blood:
3	chr14:35759553..35761751-chr14:35821894..35823859,2	MCF-7	breast:
4	chr14:35821242..35825606-chr14:35828536..35833513,6	K562	blood:
5	chr14:35782340..35785234-chr14:35821689..35824167,2	K562	blood:

Variant related genes	Relation type
ENSG00000100902	Chromatin interaction
ENSG00000265530	Chromatin interaction
ENSG00000258860	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10083375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10132397	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135435	0.89[EUR][1000 genomes]
rs10136627	0.91[EUR][1000 genomes]
rs10140133	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10140922	0.96[CEU][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs10146008	0.88[ASN][1000 genomes]
rs10146017	0.88[ASN][1000 genomes]
rs10148567	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10162508	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10438062	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11156884	0.85[EUR][1000 genomes]
rs11625311	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12385925	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12435379	0.90[EUR][1000 genomes]
rs12436216	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1475045	0.84[EUR][1000 genomes]
rs1885151	0.88[ASN][1000 genomes]
rs2006074	0.84[ASN][1000 genomes]
rs2006075	0.88[ASN][1000 genomes]
rs28589517	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28627414	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899835	0.84[ASN][1000 genomes]
rs4981283	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs4981285	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4981288	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs4982255	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4982258	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982260	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982261	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982262	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982265	0.80[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4982267	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs4982268	0.93[EUR][1000 genomes]
rs55746125	0.87[ASN][1000 genomes]
rs57645874	0.91[EUR][1000 genomes]
rs58519555	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72666622	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72666634	0.94[EUR][1000 genomes]
rs762010	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8003074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322950	0.83[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	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	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
3	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
4	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
5	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
6	nsv456205	chr14:35772940-35826370	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv564318	chr14:35772940-35826370	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv1829386	chr14:35789740-35845927	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv518090	chr14:35802483-35840241	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10135277	LCE2D	trans	parietal	SCAN
rs10135277	TBCC	trans	cerebellum	SCAN
rs10135277	NKX2-1	cis	cerebellum	SCAN
rs10135277	SRP54	cis	lymphoblastoid	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35816600-35823400	Enhancers	Primary hematopoietic stem cells	blood
2	chr14:35817200-35834400	Weak transcription	Esophagus	oesophagus
3	chr14:35819400-35825400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr14:35820800-35823400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr14:35820800-35826600	Enhancers	Fetal Intestine Small	intestine
6	chr14:35820800-35826600	Enhancers	Placenta	Placenta
7	chr14:35821000-35823400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr14:35821000-35825200	Enhancers	A549	lung
9	chr14:35821200-35823400	Enhancers	Primary T cells from cord blood	blood
10	chr14:35821400-35823400	Enhancers	Fetal Intestine Large	intestine
11	chr14:35821400-35823600	Flanking Active TSS	Liver	Liver
12	chr14:35821600-35823400	Enhancers	Hela-S3	cervix
13	chr14:35821600-35843800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr14:35821800-35824600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr14:35821800-35825000	Enhancers	HepG2	liver
16	chr14:35822000-35823400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr14:35822000-35823600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr14:35822000-35825200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr14:35822000-35825200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr14:35822000-35825200	Weak transcription	HUVEC	blood vessel
21	chr14:35822200-35826000	Enhancers	Stomach Mucosa	stomach
22	chr14:35822200-35831600	Weak transcription	Colonic Mucosa	Colon
23	chr14:35822400-35823400	Enhancers	Spleen	Spleen
24	chr14:35822400-35825000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr14:35822400-35825200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr14:35822400-35825200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr14:35822400-35825200	Weak transcription	Lung	lung
28	chr14:35822400-35825200	Weak transcription	Pancreas	Pancrea
29	chr14:35822400-35825200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr14:35822400-35825600	Weak transcription	Fetal Kidney	kidney
31	chr14:35822400-35827200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr14:35822400-35832000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr14:35822400-35832200	Weak transcription	Right Atrium	heart
34	chr14:35822400-35834400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr14:35822400-35834600	Weak transcription	Gastric	stomach
36	chr14:35822600-35825000	Weak transcription	Fetal Lung	lung
37	chr14:35822600-35825200	Weak transcription	Fetal Heart	heart
38	chr14:35822600-35825400	Weak transcription	Thymus	Thymus
39	chr14:35822600-35831600	Weak transcription	Adipose Nuclei	Adipose
40	chr14:35822600-35836400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr14:35822800-35825000	Weak transcription	GM12878-XiMat	blood
42	chr14:35822800-35825200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr14:35822800-35825200	Weak transcription	Left Ventricle	heart
44	chr14:35822800-35831600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr14:35823000-35823400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr14:35823000-35823400	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr14:35823000-35824600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr14:35823000-35825200	Weak transcription	Fetal Thymus	thymus
49	chr14:35823000-35831600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr14:35823200-35824600	Weak transcription	Rectal Mucosa Donor 29	rectum

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