Variant report

Variant	rs17617027
Chromosome Location	chr8:8388307-8388308
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8384527..8386241-chr8:8388279..8389863,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10099571	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10101904	1.00[ASN][1000 genomes]
rs10110708	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10503376	1.00[ASN][1000 genomes]
rs11989467	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11991607	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11992599	1.00[ASN][1000 genomes]
rs13248908	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13251924	1.00[ASN][1000 genomes]
rs13253870	1.00[ASN][1000 genomes]
rs13255451	1.00[ASN][1000 genomes]
rs13259482	1.00[ASN][1000 genomes]
rs13262476	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13265046	1.00[ASN][1000 genomes]
rs13269433	1.00[ASN][1000 genomes]
rs13272624	1.00[ASN][1000 genomes]
rs13280653	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1522840	1.00[ASN][1000 genomes]
rs17604776	1.00[CHB][hapmap]
rs17607697	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17618598	1.00[ASN][1000 genomes]
rs17618723	1.00[ASN][1000 genomes]
rs17626703	1.00[ASN][1000 genomes]
rs17627019	1.00[ASN][1000 genomes]
rs17669632	1.00[ASN][1000 genomes]
rs17670522	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17681846	1.00[ASN][1000 genomes]
rs17682402	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2177255	1.00[ASN][1000 genomes]
rs2976956	1.00[CHB][hapmap]
rs2976958	1.00[CHB][hapmap]
rs34353415	1.00[ASN][1000 genomes]
rs34419947	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34517137	1.00[ASN][1000 genomes]
rs34675013	1.00[ASN][1000 genomes]
rs35144760	1.00[ASN][1000 genomes]
rs35190619	1.00[ASN][1000 genomes]
rs35231847	1.00[ASN][1000 genomes]
rs35571623	1.00[ASN][1000 genomes]
rs4840966	1.00[ASN][1000 genomes]
rs4840969	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4840970	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4840971	1.00[ASN][1000 genomes]
rs4840975	1.00[ASN][1000 genomes]
rs55817265	1.00[ASN][1000 genomes]
rs6601693	1.00[CHB][hapmap]
rs66599721	1.00[ASN][1000 genomes]
rs6983300	1.00[ASN][1000 genomes]
rs6991227	1.00[ASN][1000 genomes]
rs6994016	1.00[ASN][1000 genomes]
rs7001925	1.00[ASN][1000 genomes]
rs7010670	1.00[ASN][1000 genomes]
rs7014601	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs71513198	1.00[ASN][1000 genomes]
rs71514503	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:39 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv465448	chr8:8098079-8403142	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats 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	16 gene(s)	inside rSNPs	diseases
3	nsv610152	chr8:8098079-8403142	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv610153	chr8:8098079-8454531	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1029268	chr8:8130629-8403435	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv539446	chr8:8130629-8403435	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
11	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv1019613	chr8:8239352-8636357	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv539452	chr8:8239352-8636357	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv465452	chr8:8313010-8450761	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv610173	chr8:8313010-8450761	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv465453	chr8:8318850-8439068	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv610174	chr8:8318850-8439068	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	nsv470182	chr8:8318850-8448429	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	nsv465454	chr8:8318850-8448688	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
20	nsv465455	chr8:8318850-8448688	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	nsv610175	chr8:8318850-8448688	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv465456	chr8:8318850-8450761	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	nsv465457	chr8:8318850-8450761	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv610176	chr8:8318850-8450761	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv610177	chr8:8318850-8454531	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
26	nsv1026251	chr8:8319925-8448688	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
27	nsv1025433	chr8:8324419-8432339	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
28	nsv1020159	chr8:8324419-8450231	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
29	nsv539455	chr8:8324419-8450231	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
30	nsv890333	chr8:8328101-8456563	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
31	nsv890334	chr8:8328101-8471348	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
32	esv2757256	chr8:8337819-8411145	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
33	esv2759590	chr8:8337819-8411145	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
34	nsv465458	chr8:8341105-8415810	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
35	nsv610178	chr8:8341105-8415810	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
36	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
37	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
38	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
39	esv3478821	chr8:8384142-8388440	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17617027	TDH	cis	parietal	SCAN
rs17617027	PPP1R3B	cis	cerebellum	SCAN
rs17617027	DENND2A	trans	cerebellum	SCAN
rs17617027	RP1L1	cis	parietal	SCAN
rs17617027	PRSS55	cis	cerebellum	SCAN
rs17617027	CLDN23	cis	multi-tissue	Pritchard
rs17617027	FLJ10661	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8385200-8388600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr8:8385600-8389000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr8:8385600-8394000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:8386600-8389200	Enhancers	Ovary	ovary
5	chr8:8387000-8389200	Enhancers	HepG2	liver
6	chr8:8387200-8388600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr8:8387200-8388800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:8387200-8389000	Enhancers	Fetal Heart	heart
9	chr8:8387200-8389200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:8387200-8389600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:8387400-8389000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr8:8387400-8389200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr8:8387400-8389400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr8:8387400-8389400	Enhancers	Fetal Muscle Leg	muscle
15	chr8:8387400-8389400	Enhancers	HSMMtube	muscle
16	chr8:8387600-8388800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr8:8387800-8388400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr8:8387800-8388400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:8387800-8388400	Enhancers	Left Ventricle	heart
20	chr8:8387800-8388800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr8:8387800-8389200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr8:8387800-8389200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr8:8387800-8389200	Enhancers	Placenta	Placenta
24	chr8:8387800-8389200	Enhancers	Pancreas	Pancrea
25	chr8:8388000-8388400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr8:8388000-8388400	Enhancers	Brain Substantia Nigra	brain
27	chr8:8388000-8388400	Enhancers	NHLF	lung
28	chr8:8388000-8388600	Enhancers	Brain Anterior Caudate	brain
29	chr8:8388000-8388600	Enhancers	Brain Cingulate Gyrus	brain
30	chr8:8388000-8388600	Enhancers	Fetal Kidney	kidney
31	chr8:8388000-8388600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr8:8388000-8388600	Enhancers	HUVEC	blood vessel
33	chr8:8388000-8388800	Enhancers	Osteobl	bone
34	chr8:8388000-8389000	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr8:8388000-8389000	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr8:8388000-8389000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr8:8388000-8389000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr8:8388000-8389000	Enhancers	Liver	Liver
39	chr8:8388000-8389000	Enhancers	Fetal Lung	lung
40	chr8:8388000-8389000	Weak transcription	Lung	lung
41	chr8:8388000-8389000	Enhancers	NHDF-Ad	bronchial
42	chr8:8388000-8389200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr8:8388000-8389200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr8:8388000-8389200	Enhancers	A549	lung
45	chr8:8388000-8389200	Enhancers	HSMM	muscle
46	chr8:8388000-8389400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr8:8388000-8389800	Enhancers	H9 Cell Line	embryonic stem cell
48	chr8:8388200-8388400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr8:8388200-8388400	Flanking Active TSS	NH-A	brain
50	chr8:8388200-8388600	Enhancers	Brain Hippocampus Middle	brain

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