Variant report

Variant	rs11996455
Chromosome Location	chr8:95853708-95853709
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:95845660..95850054-chr8:95850479..95855714,7	K562	blood:
2	chr8:95835030..95837351-chr8:95851254..95853830,2	MCF-7	breast:
3	chr8:95833897..95837178-chr8:95852346..95854936,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164941	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10086284	0.86[CHB][hapmap]
rs10096090	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10098563	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10098778	0.86[CHB][hapmap];0.82[GIH][hapmap]
rs10099941	0.86[CHB][hapmap]
rs10100651	0.88[ASN][1000 genomes]
rs10104909	0.86[CHB][hapmap]
rs10112232	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10441538	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10956930	0.86[CHB][hapmap]
rs10956931	0.86[CHB][hapmap]
rs10956932	0.86[CHB][hapmap]
rs1129152	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12155666	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12545815	0.86[ASN][1000 genomes]
rs12548874	0.83[EUR][1000 genomes]
rs12548999	0.86[CHB][hapmap]
rs12549003	0.86[CHB][hapmap]
rs12550765	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs12679044	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs13271375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13271644	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1453377	0.86[CHB][hapmap]
rs1453379	0.86[CHB][hapmap]
rs16893776	0.86[CHB][hapmap];0.82[GIH][hapmap]
rs2123647	0.86[CHB][hapmap]
rs2945554	0.86[CHB][hapmap]
rs3779789	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802193	0.86[CHB][hapmap]
rs4073755	0.86[ASN][1000 genomes]
rs4075835	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4500055	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4734285	0.86[ASN][1000 genomes]
rs4735331	0.86[CHB][hapmap]
rs4735332	0.86[CHB][hapmap]
rs4735336	0.86[CHB][hapmap];0.82[GIH][hapmap]
rs4735337	0.86[CHB][hapmap];0.82[GIH][hapmap]
rs4735339	0.86[CHB][hapmap];0.82[GIH][hapmap]
rs6471497	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs6471503	0.86[CHB][hapmap]
rs6471504	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6982393	0.86[CHB][hapmap];0.82[GIH][hapmap]
rs6991067	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7001535	0.86[CHB][hapmap]
rs7002058	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7004862	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7015841	0.86[CHB][hapmap]
rs7017487	0.86[CHB][hapmap]
rs713113	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7817862	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7820818	0.86[CHB][hapmap]
rs7827478	0.86[CHB][hapmap]
rs7845219	0.86[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap]
rs896854	0.84[GIH][hapmap]
rs9643349	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9650133	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11996455	PLEKHF2	cis	parietal	SCAN
rs11996455	TP53INP1	Cis_1M	lymphoblastoid	RTeQTL
rs11996455	RAD54B	cis	cerebellum	SCAN
rs11996455	INTS8	cis	cerebellum	SCAN
rs11996455	RBM12B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95836800-95866800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr8:95836800-95874600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:95837000-95905600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr8:95837400-95898800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr8:95837600-95869800	Weak transcription	Psoas Muscle	Psoas
6	chr8:95838200-95905600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:95838600-95860400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr8:95838800-95876000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr8:95839400-95854800	Strong transcription	Fetal Thymus	thymus
10	chr8:95839400-95857800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr8:95839400-95859600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr8:95839400-95872200	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr8:95839400-95872400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr8:95839400-95872400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr8:95839400-95872400	Strong transcription	Dnd41	blood
16	chr8:95839400-95872600	Strong transcription	Liver	Liver
17	chr8:95839400-95872600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr8:95839400-95904400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr8:95839600-95854600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr8:95839600-95858000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr8:95839600-95863200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr8:95839600-95873400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr8:95839600-95873400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr8:95840200-95853800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr8:95840200-95860600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr8:95840400-95855400	Strong transcription	Primary B cells from cord blood	blood
27	chr8:95840600-95860600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr8:95840600-95873000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr8:95840800-95860600	Strong transcription	Adipose Nuclei	Adipose
30	chr8:95842800-95857200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr8:95843800-95858600	Weak transcription	Small Intestine	intestine
32	chr8:95844000-95859400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr8:95845200-95858200	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr8:95845200-95860800	Strong transcription	Fetal Intestine Large	intestine
35	chr8:95845600-95860600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr8:95845600-95862800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr8:95845800-95872600	Strong transcription	Placenta	Placenta
38	chr8:95846000-95858200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr8:95846400-95858200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr8:95846400-95858600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr8:95846600-95855000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr8:95847000-95854800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr8:95847000-95856600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr8:95847200-95854600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr8:95847200-95856200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr8:95847400-95873000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr8:95847400-95890800	Weak transcription	Stomach Mucosa	stomach
48	chr8:95848400-95859400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr8:95848400-95873000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr8:95848600-95856400	Weak transcription	Right Ventricle	heart

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