Variant report

Variant	rs2700
Chromosome Location	chr14:20825965-20825966
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:20795547..20797603-chr14:20824363..20826588,2	K562	blood:
2	chr14:20809897..20813381-chr14:20823524..20827429,6	MCF-7	breast:
3	chr14:20821465..20823482-chr14:20825881..20827740,3	K562	blood:

Variant related genes	Relation type
ENSG00000100814	Chromatin interaction
ENSG00000129484	Chromatin interaction
ENSG00000259001	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10129957	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10130660	0.99[ASN][1000 genomes]
rs10147163	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10148359	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12323412	0.93[ASN][1000 genomes]
rs12323610	0.93[ASN][1000 genomes]
rs12891805	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2104977	1.00[YRI][hapmap]
rs2297616	0.84[ASW][hapmap];0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3093872	0.85[LWK][hapmap]
rs3093882	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3093890	0.84[ASW][hapmap];0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3093897	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3093900	0.87[AFR][1000 genomes]
rs3093902	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3093904	0.90[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3093907	0.90[GIH][hapmap]
rs3093933	1.00[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3093939	1.00[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs3093940	1.00[YRI][hapmap]
rs3093942	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34848586	0.99[ASN][1000 genomes]
rs4415933	0.95[ASN][1000 genomes]
rs4981150	0.85[CHB][hapmap]
rs4981153	0.81[CHB][hapmap]
rs4981158	0.93[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4981983	0.83[EUR][1000 genomes]
rs4981998	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57101853	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58530849	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59821173	0.99[ASN][1000 genomes]
rs6575135	0.86[CHB][hapmap];0.88[GIH][hapmap]
rs7155699	0.84[ASW][hapmap];0.81[GIH][hapmap]
rs7161611	0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs8009242	0.86[CHB][hapmap];0.88[GIH][hapmap]
rs8022565	0.86[CHB][hapmap];0.88[GIH][hapmap]
rs878157	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs884368	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers 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	203 gene(s)	inside rSNPs	diseases
2	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
3	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
4	nsv541974	chr14:20517485-20901811	Enhancers Active TSS 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 Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
5	esv1806993	chr14:20743269-20841162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	nsv534131	chr14:20757405-20886235	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	esv21015	chr14:20800765-21257878	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2700	RPPH1	cis	multi-tissue	Pritchard
rs2700	JUB	cis	cerebellum	SCAN
rs2700	RPPH1	cis	lymphoblastoid	seeQTL
rs2700	CCNB1IP1	cis	parietal	SCAN
rs2700	TTC5	cis	cerebellum	SCAN
rs2700	PARP2	cis	cerebellum	SCAN
rs2700	PARP2	cis	parietal	SCAN
rs2700	CCNB1IP1	cis	cerebellum	SCAN
rs2700	PARP2	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20812400-20880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:20812600-20831800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:20812600-20834600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr14:20812600-20841000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr14:20812600-20845600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr14:20813000-20827000	Strong transcription	Fetal Muscle Trunk	muscle
7	chr14:20813000-20827800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr14:20813000-20827800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr14:20813000-20830800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:20813200-20826200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr14:20813200-20826600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:20813200-20826800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr14:20813200-20827000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr14:20813200-20827000	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr14:20813200-20827400	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr14:20813200-20827600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:20813200-20827600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:20813200-20827800	Strong transcription	Fetal Intestine Large	intestine
19	chr14:20813200-20827800	Strong transcription	Placenta	Placenta
20	chr14:20813200-20828000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr14:20813200-20828400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr14:20813200-20829400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr14:20813200-20831600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr14:20813200-20869200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr14:20813400-20826000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr14:20813400-20826400	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr14:20813400-20826600	Strong transcription	Fetal Muscle Leg	muscle
28	chr14:20813400-20826600	Strong transcription	Left Ventricle	heart
29	chr14:20813400-20827200	Strong transcription	Brain Anterior Caudate	brain
30	chr14:20813400-20827400	Strong transcription	Brain Hippocampus Middle	brain
31	chr14:20813400-20827800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr14:20813400-20827800	Strong transcription	Liver	Liver
33	chr14:20813400-20828600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr14:20813400-20829000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr14:20813600-20826200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr14:20813600-20826800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr14:20813600-20827000	Strong transcription	Hela-S3	cervix
38	chr14:20813600-20827600	Strong transcription	Adipose Nuclei	Adipose
39	chr14:20813600-20827800	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr14:20813600-20827800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr14:20813600-20827800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr14:20813600-20827800	Strong transcription	HSMM	muscle
43	chr14:20814200-20827200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr14:20814200-20827600	Strong transcription	Dnd41	blood
45	chr14:20814800-20826000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr14:20814800-20826600	Strong transcription	GM12878-XiMat	blood
47	chr14:20815000-20827400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr14:20815200-20826400	Strong transcription	Brain Substantia Nigra	brain
49	chr14:20815200-20826800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr14:20815200-20827800	Strong transcription	Osteobl	bone

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