Variant report

Variant	rs10441538
Chromosome Location	chr8:95868608-95868609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:95867874-95869025	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:95866839..95869390-chr8:95887943..95889546,2	MCF-7	breast:
2	chr8:95866505..95869055-chr8:95873345..95875262,2	MCF-7	breast:

Variant related genes	Relation type
INTS8	TF binding region
ENSG00000164941	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10086284	0.84[CHB][hapmap]
rs10096090	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10098563	0.80[EUR][1000 genomes]
rs10098778	0.84[CHB][hapmap]
rs10099941	0.84[CHB][hapmap]
rs10100651	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10104909	0.84[CHB][hapmap]
rs10112232	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10956930	0.84[CHB][hapmap]
rs10956931	0.84[CHB][hapmap]
rs10956932	0.84[CHB][hapmap]
rs1129152	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs11996455	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]
rs12155666	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12545815	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12548874	0.81[ASN][1000 genomes]
rs12548999	0.84[CHB][hapmap]
rs12549003	0.84[CHB][hapmap]
rs12550765	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs12679044	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13271375	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13271644	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1453377	0.84[CHB][hapmap]
rs1453379	0.84[CHB][hapmap]
rs16893776	0.84[CHB][hapmap]
rs2123647	0.84[CHB][hapmap]
rs2945554	0.84[CHB][hapmap]
rs3779789	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3802193	0.84[CHB][hapmap]
rs4073755	0.81[ASN][1000 genomes]
rs4075835	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4500055	0.96[CEU][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4734285	0.93[ASN][1000 genomes]
rs4734291	0.83[GIH][hapmap]
rs4735331	0.84[CHB][hapmap]
rs4735332	0.84[CHB][hapmap]
rs4735336	0.84[CHB][hapmap]
rs4735337	0.84[CHB][hapmap]
rs4735339	0.84[CHB][hapmap]
rs477653	0.82[CHB][hapmap]
rs550418	0.84[CHB][hapmap]
rs550564	0.84[CHB][hapmap]
rs6471497	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6471503	0.84[CHB][hapmap]
rs6471504	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs683832	0.84[CHB][hapmap]
rs6982393	0.84[CHB][hapmap]
rs6991067	0.96[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];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7001535	0.84[CHB][hapmap]
rs7002058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7004862	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7015841	0.84[CHB][hapmap]
rs7017487	0.84[CHB][hapmap]
rs713113	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7817862	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7820818	0.84[CHB][hapmap]
rs7827478	0.84[CHB][hapmap]
rs7845219	0.84[CHB][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap]
rs896854	0.81[GIH][hapmap]
rs9643349	0.82[ASN][1000 genomes]
rs9650133	0.88[EUR][1000 genomes];0.88[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10441538	RAD54B	cis	cerebellum	SCAN
rs10441538	PLEKHF2	cis	parietal	SCAN
rs10441538	LAPTM4B	cis	parietal	SCAN
rs10441538	RBM12B	cis	cerebellum	SCAN
rs10441538	INTS8	Cis_1M	lymphoblastoid	RTeQTL
rs10441538	TP53INP1	cis	parietal	SCAN
rs10441538	TP53INP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95836800-95874600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:95837000-95905600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:95837400-95898800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:95837600-95869800	Weak transcription	Psoas Muscle	Psoas
5	chr8:95838200-95905600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:95838800-95876000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr8:95839400-95872200	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr8:95839400-95872400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr8:95839400-95872400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr8:95839400-95872400	Strong transcription	Dnd41	blood
11	chr8:95839400-95872600	Strong transcription	Liver	Liver
12	chr8:95839400-95872600	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr8:95839400-95904400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:95839600-95873400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr8:95839600-95873400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr8:95840600-95873000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr8:95845800-95872600	Strong transcription	Placenta	Placenta
18	chr8:95847400-95873000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr8:95847400-95890800	Weak transcription	Stomach Mucosa	stomach
20	chr8:95848400-95873000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr8:95848800-95869000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:95849800-95872200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr8:95849800-95873000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr8:95850400-95872600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr8:95850600-95872600	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr8:95851400-95869000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr8:95851400-95870000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr8:95851400-95871800	Weak transcription	Fetal Heart	heart
29	chr8:95851600-95874200	Weak transcription	Pancreas	Pancrea
30	chr8:95854600-95872400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr8:95855600-95873800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr8:95855600-95874200	Strong transcription	Fetal Thymus	thymus
33	chr8:95855800-95873000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr8:95856800-95872600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr8:95857000-95869400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr8:95857200-95872200	Strong transcription	Fetal Lung	lung
37	chr8:95857600-95868800	Weak transcription	Right Ventricle	heart
38	chr8:95858800-95872200	Strong transcription	HSMM	muscle
39	chr8:95859000-95872400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr8:95859400-95869600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr8:95859400-95872600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr8:95860000-95872200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr8:95860000-95873000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr8:95860600-95868800	Weak transcription	Gastric	stomach
45	chr8:95860600-95873000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr8:95861000-95881400	Strong transcription	GM12878-XiMat	blood
47	chr8:95861400-95872200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr8:95861400-95873000	Strong transcription	Primary T cells from cord blood	blood
49	chr8:95861400-95874000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr8:95861400-95874200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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