Variant report

Variant	rs1630656
Chromosome Location	chr17:17161887-17161888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17161075..17162891-chr17:17166950..17169693,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12453455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600589	0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12949822	0.81[ASN][1000 genomes]
rs1708617	0.94[ASN][1000 genomes]
rs1708621	0.94[ASN][1000 genomes]
rs1708624	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708628	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1736204	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1736205	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1736208	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs1736209	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs1736211	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1736212	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1736216	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1736217	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs1736221	0.93[ASN][1000 genomes]
rs2012954	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2018781	0.94[ASN][1000 genomes]
rs2292527	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2472689	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36079048	0.90[ASN][1000 genomes]
rs3866959	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985760	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066065	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62066066	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6502564	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6502568	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502569	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502570	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502571	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7217560	0.80[MEX][hapmap];0.81[TSI][hapmap]
rs7220577	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220827	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs7221553	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7224598	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7225876	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066090	0.94[ASN][1000 genomes]
rs8080386	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9892352	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894565	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065811	chr17:17104760-17225204	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1630656	SMCR8	cis	cerebellum	SCAN
rs1630656	FLCN	cis	parietal	SCAN
rs1630656	TOM1L2	cis	cerebellum	SCAN
rs1630656	FLCN	cis	cerebellum	SCAN
rs1630656	ULK2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17141800-17162200	Weak transcription	Stomach Mucosa	stomach
2	chr17:17146000-17171000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:17148600-17167400	Strong transcription	Fetal Intestine Small	intestine
4	chr17:17148600-17172000	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr17:17148600-17178800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr17:17148600-17179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:17148600-17179600	Strong transcription	Fetal Muscle Trunk	muscle
8	chr17:17148600-17180000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:17148800-17178400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:17148800-17178400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr17:17148800-17179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr17:17148800-17179600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr17:17148800-17179600	Strong transcription	Fetal Muscle Leg	muscle
14	chr17:17148800-17179800	Strong transcription	Fetal Stomach	stomach
15	chr17:17148800-17180200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:17148800-17180400	Strong transcription	Fetal Thymus	thymus
17	chr17:17149000-17165200	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr17:17149000-17165600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr17:17149000-17165600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr17:17149000-17165600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:17149000-17165800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr17:17149000-17165800	Strong transcription	Fetal Brain Female	brain
23	chr17:17149000-17166000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:17149000-17174800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr17:17149000-17174800	Strong transcription	Adipose Nuclei	Adipose
26	chr17:17149000-17174800	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr17:17149000-17178400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr17:17149000-17178800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:17149000-17179200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr17:17149000-17179400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr17:17149000-17180800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr17:17149000-17181200	Strong transcription	Dnd41	blood
33	chr17:17149200-17164000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr17:17149200-17164000	Strong transcription	Rectal Smooth Muscle	rectum
35	chr17:17149200-17171400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr17:17149200-17177400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr17:17149200-17179000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr17:17149200-17179600	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr17:17149200-17179600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr17:17149200-17179800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr17:17149400-17174400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr17:17149400-17175000	Strong transcription	Thymus	Thymus
43	chr17:17149400-17179600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr17:17149400-17179600	Strong transcription	Placenta	Placenta
45	chr17:17149600-17174800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr17:17149800-17179000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr17:17150000-17180000	Strong transcription	Primary T cells from cord blood	blood
48	chr17:17150200-17179400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr17:17150200-17179800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr17:17152200-17162000	Weak transcription	Small Intestine	intestine

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