Variant report

Variant	rs12599391
Chromosome Location	chr16:69605349-69605350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69598845..69601528-chr16:69603220..69607437,4	MCF-7	breast:
2	chr16:69604663..69607027-chr16:69622844..69624484,2	K562	blood:
3	chr16:69603757..69608003-chr16:69608189..69613154,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102908	Chromatin interaction
ENSG00000223109	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11075729	0.84[AFR][1000 genomes]
rs11640319	0.83[ASW][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs12923231	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12924052	0.89[YRI][hapmap]
rs12929503	0.88[EUR][1000 genomes]
rs12933292	0.89[EUR][1000 genomes]
rs13330951	0.90[JPT][hapmap];0.83[MEX][hapmap]
rs1364063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1437134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1469908	0.82[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs2032912	0.89[EUR][1000 genomes]
rs2161630	0.83[ASW][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs244415	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs244417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs244418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs244420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2917670	0.87[LWK][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap]
rs2917677	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35967356	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3848278	0.83[ASW][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs4633710	0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs4783721	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4783722	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62052815	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62052816	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6499240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6499244	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs669696	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7187634	0.83[ASW][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs7191292	0.83[ASW][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs7192380	0.83[ASW][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs7205551	0.84[AFR][1000 genomes]
rs73568391	0.81[AFR][1000 genomes]
rs7359336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8049728	0.83[ASW][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs8055756	0.81[ASW][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs8061052	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs862320	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs889398	0.96[CEU][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs889399	0.96[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs9938213	0.84[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1852	chr16:69566121-69610962	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12599391	PDXDC2P	cis	parietal	SCAN
rs12599391	COG8	cis	cerebellum	SCAN
rs12599391	HSF4	cis	cerebellum	SCAN
rs12599391	TPPP3	cis	cerebellum	SCAN
rs12599391	DUS2L	cis	cerebellum	SCAN
rs12599391	LCAT	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69601400-69613000	Weak transcription	Small Intestine	intestine
2	chr16:69601600-69610600	Weak transcription	Ovary	ovary
3	chr16:69601800-69605400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr16:69601800-69610600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr16:69602000-69606000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr16:69602000-69610600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr16:69602000-69633000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr16:69602200-69605400	Enhancers	Rectal Smooth Muscle	rectum
9	chr16:69602200-69605600	Weak transcription	Colonic Mucosa	Colon
10	chr16:69602200-69609200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr16:69602200-69610400	Weak transcription	Placenta	Placenta
12	chr16:69602200-69610400	Weak transcription	Lung	lung
13	chr16:69602200-69619400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr16:69602200-69622000	Weak transcription	Gastric	stomach
15	chr16:69602200-69627000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr16:69602200-69628600	Weak transcription	Right Atrium	heart
17	chr16:69602200-69631600	Weak transcription	Pancreas	Pancrea
18	chr16:69602200-69643200	Weak transcription	Fetal Muscle Leg	muscle
19	chr16:69602200-69646600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr16:69602200-69653600	Weak transcription	Fetal Thymus	thymus
21	chr16:69602400-69605600	Strong transcription	HSMM	muscle
22	chr16:69602400-69610400	Weak transcription	Psoas Muscle	Psoas
23	chr16:69602600-69607600	Weak transcription	Fetal Intestine Small	intestine
24	chr16:69602600-69609000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:69602600-69610600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr16:69602600-69614200	Weak transcription	Fetal Stomach	stomach
27	chr16:69602600-69628600	Weak transcription	Thymus	Thymus
28	chr16:69602600-69628800	Weak transcription	Right Ventricle	heart
29	chr16:69602600-69629600	Weak transcription	HSMMtube	muscle
30	chr16:69602600-69630200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr16:69602600-69630800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr16:69602800-69605600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr16:69602800-69608800	Weak transcription	Fetal Intestine Large	intestine
34	chr16:69602800-69610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr16:69602800-69611400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr16:69602800-69627800	Weak transcription	Fetal Kidney	kidney
37	chr16:69602800-69629200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr16:69603000-69610600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr16:69603000-69613400	Weak transcription	Fetal Heart	heart
40	chr16:69603000-69617400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr16:69603000-69627800	Weak transcription	Brain Substantia Nigra	brain
42	chr16:69603000-69647400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr16:69603200-69606200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr16:69603200-69606800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr16:69603200-69610600	Weak transcription	Brain Angular Gyrus	brain
46	chr16:69603200-69612000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr16:69603200-69627800	Weak transcription	Primary B cells from cord blood	blood
48	chr16:69603200-69629600	Weak transcription	NH-A	brain
49	chr16:69603400-69614600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr16:69603400-69617200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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