Variant report

Variant	rs9912109
Chromosome Location	chr17:17215582-17215583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17183013..17185688-chr17:17214921..17217867,2	K562	blood:
2	chr17:17207055..17208999-chr17:17214902..17216506,2	MCF-7	breast:
3	chr17:17108529..17111037-chr17:17215111..17217756,2	K562	blood:

Variant related genes	Relation type
ENSG00000179598	Chromatin interaction
ENSG00000141030	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12451886	0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs12949216	0.92[ASN][1000 genomes]
rs12950929	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2041393	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6502577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6502578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7207856	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7217114	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7217162	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9889367	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9889738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9895057	0.81[ASN][1000 genomes]
rs9896977	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9899615	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs9907711	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9907857	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9908360	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9908807	0.81[ASN][1000 genomes]
rs9909111	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9909850	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1061186	chr17:17200427-17314406	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9912109	TNFRSF13B	cis	cerebellum	SCAN
rs9912109	FLCN	cis	lymphoblastoid	seeQTL
rs9912109	FLII	cis	parietal	SCAN
rs9912109	COPS3	cis	multi-tissue	Pritchard

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17207400-17235400	Weak transcription	Lung	lung
2	chr17:17207600-17217800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr17:17207600-17246400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:17207800-17216600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:17207800-17216800	Weak transcription	Fetal Intestine Large	intestine
6	chr17:17207800-17226400	Weak transcription	Brain Angular Gyrus	brain
7	chr17:17207800-17228000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr17:17207800-17228000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr17:17207800-17228400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr17:17207800-17229600	Weak transcription	Adipose Nuclei	Adipose
11	chr17:17207800-17243400	Weak transcription	Colon Smooth Muscle	Colon
12	chr17:17208000-17216800	Weak transcription	Left Ventricle	heart
13	chr17:17208000-17218600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr17:17208000-17226000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr17:17208000-17226200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr17:17208200-17216600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr17:17208200-17216800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr17:17208200-17225400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr17:17208200-17225400	Weak transcription	Brain Anterior Caudate	brain
20	chr17:17208200-17226400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr17:17208200-17228200	Weak transcription	Brain Hippocampus Middle	brain
22	chr17:17208400-17216800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr17:17208400-17225400	Weak transcription	Brain Germinal Matrix	brain
24	chr17:17208600-17255400	Weak transcription	Brain Substantia Nigra	brain
25	chr17:17208800-17236000	Weak transcription	Right Ventricle	heart
26	chr17:17209000-17217600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr17:17209000-17226000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr17:17209000-17227600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr17:17209200-17224000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr17:17209200-17224600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr17:17209400-17216800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr17:17209600-17217000	Weak transcription	Fetal Heart	heart
33	chr17:17209800-17216800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr17:17209800-17216800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr17:17209800-17216800	Weak transcription	A549	lung
36	chr17:17209800-17217800	Weak transcription	Thymus	Thymus
37	chr17:17209800-17226400	Weak transcription	Fetal Intestine Small	intestine
38	chr17:17210000-17217800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr17:17210000-17218000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr17:17210200-17216800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr17:17210200-17216800	Weak transcription	Fetal Thymus	thymus
42	chr17:17210200-17217800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr17:17210400-17215800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr17:17210600-17216800	Weak transcription	Fetal Muscle Leg	muscle
45	chr17:17210600-17233400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:17210800-17216200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr17:17212000-17219000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr17:17212400-17229000	Weak transcription	Fetal Brain Male	brain
49	chr17:17213000-17218600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr17:17213000-17248000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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