Variant report

Variant	rs17653841
Chromosome Location	chr8:8998022-8998023
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	chr8:8997466-8999259	K562	blood:	n/a	n/a
2	MAX	chr8:8997512-8998030	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr8:8997381-8998190	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr8:8991597-8999830	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr8:8997364-8998081	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr8:8998019-8998067	GM12878	blood:	n/a	n/a
7	POLR2A	chr8:8997288-8998045	HUVEC	blood vessel:	n/a	n/a
8	FOXP2	chr8:8997402-8998208	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000254340	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1121782	0.91[EUR][1000 genomes]
rs17155176	0.80[MEX][hapmap]
rs17155250	0.91[EUR][1000 genomes]
rs17155257	0.92[EUR][1000 genomes]
rs34475063	0.84[EUR][1000 genomes]
rs34986822	0.91[EUR][1000 genomes]
rs4269548	0.91[EUR][1000 genomes]
rs4307346	0.91[EUR][1000 genomes]
rs55888332	0.91[EUR][1000 genomes]
rs57232711	0.91[EUR][1000 genomes]
rs6989093	0.91[EUR][1000 genomes]
rs6997764	0.86[EUR][1000 genomes]
rs7005776	0.91[EUR][1000 genomes]
rs7011104	0.91[EUR][1000 genomes]
rs7819120	0.90[EUR][1000 genomes]
rs7834628	0.91[EUR][1000 genomes]
rs7835704	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1022328	chr8:8954003-9061281	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv610206	chr8:8961017-9162048	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1026279	chr8:8982622-9030279	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	n/a
8	nsv949434	chr8:8993551-9318404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv3478829	chr8:8997814-8998159	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	n/a
10	esv3478828	chr8:8997872-8998117	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	n/a
11	esv3478831	chr8:8997886-8998113	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17653841	MSRA	cis	parietal	SCAN
rs17653841	THEX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8992600-9000000	Weak transcription	Hela-S3	cervix
2	chr8:8993600-9005400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr8:8993800-8998400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:8993800-8998600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr8:8993800-9007400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr8:8994200-9000800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr8:8994200-9005600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr8:8994200-9007200	Weak transcription	Brain Angular Gyrus	brain
9	chr8:8994200-9007200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr8:8994200-9007200	Weak transcription	Fetal Brain Male	brain
11	chr8:8994400-8998400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr8:8994400-9001000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr8:8994400-9005200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr8:8994400-9005200	Weak transcription	Small Intestine	intestine
15	chr8:8994600-8999600	Genic enhancers	HUVEC	blood vessel
16	chr8:8994600-9000400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr8:8994800-8998200	Genic enhancers	Fetal Intestine Large	intestine
18	chr8:8994800-8998600	Genic enhancers	Fetal Intestine Small	intestine
19	chr8:8994800-8999800	Strong transcription	Fetal Stomach	stomach
20	chr8:8994800-8999800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr8:8994800-9000000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr8:8994800-9000600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr8:8994800-9001000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr8:8994800-9001000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr8:8994800-9001800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr8:8995000-8999200	Strong transcription	NHDF-Ad	bronchial
27	chr8:8995000-8999400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
28	chr8:8995000-9000600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr8:8995000-9000800	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr8:8995200-8999200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr8:8995200-8999800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr8:8995200-9000800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr8:8995200-9000800	Strong transcription	Fetal Muscle Leg	muscle
34	chr8:8995200-9004800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr8:8995400-8998400	Weak transcription	Stomach Mucosa	stomach
36	chr8:8995400-8999400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr8:8995400-9000600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr8:8995400-9001000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr8:8995600-8998400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr8:8995600-9000600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:8995800-8998800	Genic enhancers	Fetal Heart	heart
42	chr8:8996200-8999200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr8:8996200-8999600	Strong transcription	Aorta	Aorta
44	chr8:8996200-8999600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr8:8996200-8999800	Strong transcription	Primary T cells from cord blood	blood
46	chr8:8996200-9000400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr8:8996200-9000800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr8:8996200-9001800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr8:8996400-8999400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr8:8996400-8999800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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