Variant report

Variant	rs17135109
Chromosome Location	chr7:4816574-4816575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:4721460..4723337-chr7:4813356..4816619,3	MCF-7	breast:
2	chr7:4815302..4817443-chr7:4835837..4838194,2	MCF-7	breast:
3	chr7:4813279..4817996-chr7:4818432..4827499,15	MCF-7	breast:
4	chr7:4723905..4726708-chr7:4815348..4817182,2	K562	blood:
5	chr7:4815353..4817520-chr7:4819712..4821919,3	K562	blood:
6	chr7:4813801..4815751-chr7:4816573..4818278,2	MCF-7	breast:
7	chr7:4815133..4816843-chr7:4827652..4829770,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264474	Chromatin interaction
ENSG00000164916	Chromatin interaction
ENSG00000242802	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11549839	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11549840	0.90[EUR][1000 genomes]
rs11976063	1.00[CEU][hapmap]
rs11976296	1.00[CEU][hapmap]
rs17135086	1.00[CEU][hapmap]
rs17135087	1.00[CEU][hapmap]
rs17135113	1.00[CEU][hapmap]
rs17135119	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59542846	0.81[EUR][1000 genomes]
rs6949537	0.89[AMR][1000 genomes]
rs6979798	1.00[CEU][hapmap]
rs7802515	1.00[CEU][hapmap]
rs7810433	1.00[CEU][hapmap]
rs907718	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv887377	chr7:4730535-4862259	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv887378	chr7:4730535-4929721	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv887379	chr7:4749527-4828593	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv887380	chr7:4760124-4929721	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv471293	chr7:4764861-4885221	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv887381	chr7:4769030-4880954	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
11	nsv823994	chr7:4792385-4928328	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv887382	chr7:4792762-4880954	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv8033	chr7:4802287-5086597	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	nsv1022678	chr7:4810626-5113387	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
15	nsv538705	chr7:4810626-5113387	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
16	nsv482101	chr7:4815264-4831397	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17135109	SLITRK6	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4813800-4817000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:4814400-4816600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr7:4814600-4816600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:4814600-4816600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:4814800-4816600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:4815400-4816800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:4815600-4816600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
8	chr7:4815600-4816600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr7:4815600-4816600	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr7:4815600-4816600	Flanking Active TSS	Liver	Liver
11	chr7:4815600-4816600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr7:4815600-4816800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
13	chr7:4815600-4816800	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr7:4815800-4816600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr7:4815800-4816600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr7:4815800-4816600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:4815800-4816600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr7:4815800-4816600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:4815800-4816600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:4815800-4816600	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr7:4815800-4816600	Transcr. at gene 5' and 3'	K562	blood
22	chr7:4815800-4816800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:4815800-4816800	Flanking Active TSS	Dnd41	blood
24	chr7:4815800-4816800	Flanking Active TSS	Hela-S3	cervix
25	chr7:4815800-4816800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr7:4816000-4816600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:4816000-4816600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr7:4816000-4816600	Enhancers	Fetal Brain Male	brain
29	chr7:4816000-4816600	Flanking Active TSS	Lung	lung
30	chr7:4816000-4816800	Enhancers	Fetal Heart	heart
31	chr7:4816000-4816800	Enhancers	Stomach Mucosa	stomach
32	chr7:4816000-4820600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:4816000-4820600	Weak transcription	Small Intestine	intestine
34	chr7:4816000-4820800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr7:4816000-4820800	Weak transcription	Aorta	Aorta
36	chr7:4816000-4832000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr7:4816200-4816600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr7:4816200-4816600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr7:4816200-4816600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr7:4816200-4816600	Enhancers	Brain Germinal Matrix	brain
41	chr7:4816200-4816600	Flanking Active TSS	Colonic Mucosa	Colon
42	chr7:4816200-4816600	Flanking Active TSS	Fetal Intestine Large	intestine
43	chr7:4816200-4816600	Enhancers	Right Ventricle	heart
44	chr7:4816200-4816600	Flanking Active TSS	HSMM	muscle
45	chr7:4816200-4816600	Flanking Active TSS	NH-A	brain
46	chr7:4816200-4816800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr7:4816200-4816800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:4816200-4816800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:4816200-4816800	Enhancers	Brain Angular Gyrus	brain
50	chr7:4816200-4816800	Enhancers	Brain Anterior Caudate	brain

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