Variant report

Variant	rs16973190
Chromosome Location	chr16:71508501-71508502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71506966..71508827-chr16:71510994..71513448,2	MCF-7	breast:
2	chr16:71507450..71511299-chr16:71511883..71513820,5	K562	blood:
3	chr16:71501449..71503485-chr16:71506644..71509669,3	MCF-7	breast:
4	chr16:71494025..71497980-chr16:71506815..71510228,4	K562	blood:
5	chr16:71508246..71511064-chr16:71516547..71519494,2	K562	blood:
6	chr16:71498533..71500835-chr16:71506756..71508900,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157429	Chromatin interaction
ENSG00000167377	Chromatin interaction
ENSG00000247324	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10468265	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866859	1.00[ASN][1000 genomes]
rs12325234	0.90[CEU][hapmap]
rs12444714	0.81[ASW][hapmap];0.90[CEU][hapmap];0.82[TSI][hapmap]
rs12918320	0.90[CEU][hapmap];0.94[TSI][hapmap]
rs12919092	0.90[CEU][hapmap]
rs13336809	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972266	1.00[ASN][1000 genomes]
rs16972805	1.00[ASN][1000 genomes]
rs16972808	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973000	1.00[ASN][1000 genomes]
rs16973112	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973286	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1804984	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2052873	1.00[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886947	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56222754	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57821244	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59364668	0.88[EUR][1000 genomes]
rs61171207	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499520	0.89[CEU][hapmap]
rs6499521	0.81[EUR][1000 genomes]
rs7188021	1.00[ASN][1000 genomes]
rs7197127	1.00[ASN][1000 genomes]
rs72791971	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72791974	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72795864	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795867	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72795869	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795881	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797728	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8044168	1.00[ASN][1000 genomes]
rs8049040	1.00[ASN][1000 genomes]
rs8050135	1.00[ASN][1000 genomes]
rs8051439	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056735	1.00[CEU][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940485	1.00[ASN][1000 genomes]
rs9989376	0.87[EUR][1000 genomes]
rs9989377	0.96[EUR][1000 genomes];1.00[ASN][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	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs16973190	CTCF	cis	cerebellum	SCAN
rs16973190	C16orf86	cis	parietal	SCAN
rs16973190	SNTB2	cis	cerebellum	SCAN
rs16973190	ZNF19	cis	cerebellum	SCAN
rs16973190	RANBP10	cis	parietal	SCAN
rs16973190	ZNF23	cis	parietal	SCAN
rs16973190	COG4	cis	parietal	SCAN
rs16973190	CBFB	cis	parietal	SCAN
rs16973190	RP11-510M2.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71496400-71509400	Weak transcription	Small Intestine	intestine
2	chr16:71496600-71509200	Weak transcription	Fetal Intestine Large	intestine
3	chr16:71496600-71509400	Weak transcription	Colonic Mucosa	Colon
4	chr16:71496600-71509400	Weak transcription	Esophagus	oesophagus
5	chr16:71496600-71509400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr16:71496600-71511400	Weak transcription	Pancreas	Pancrea
7	chr16:71496800-71508600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr16:71496800-71508600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr16:71496800-71508600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr16:71496800-71508800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr16:71496800-71508800	Weak transcription	Primary T cells from cord blood	blood
12	chr16:71496800-71508800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr16:71496800-71508800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr16:71496800-71508800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr16:71496800-71509000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr16:71496800-71509200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr16:71496800-71509400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr16:71496800-71509400	Weak transcription	Psoas Muscle	Psoas
19	chr16:71496800-71512000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr16:71496800-71512200	Weak transcription	Fetal Intestine Small	intestine
21	chr16:71497000-71508600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr16:71497000-71511800	Weak transcription	Brain Substantia Nigra	brain
23	chr16:71497000-71517400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr16:71497000-71517400	Weak transcription	Fetal Heart	heart
25	chr16:71497000-71517600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr16:71497200-71508600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr16:71497200-71508600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr16:71497200-71509000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr16:71497200-71509200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr16:71497200-71509400	Weak transcription	Colon Smooth Muscle	Colon
31	chr16:71497200-71509400	Weak transcription	Lung	lung
32	chr16:71497400-71508800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr16:71497400-71509000	Weak transcription	Right Ventricle	heart
34	chr16:71497400-71509200	Weak transcription	Primary B cells from cord blood	blood
35	chr16:71497400-71509200	Weak transcription	Brain Angular Gyrus	brain
36	chr16:71497400-71509200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr16:71497400-71509200	Weak transcription	HepG2	liver
38	chr16:71497400-71509600	Weak transcription	Gastric	stomach
39	chr16:71497400-71509800	Weak transcription	Spleen	Spleen
40	chr16:71502800-71517400	Weak transcription	Dnd41	blood
41	chr16:71503400-71509000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr16:71503600-71509200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr16:71503800-71509400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr16:71504000-71509400	Weak transcription	Fetal Lung	lung
45	chr16:71504400-71508800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr16:71504400-71509800	Weak transcription	Fetal Kidney	kidney
47	chr16:71504400-71512800	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr16:71504600-71513600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr16:71504800-71512800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr16:71504800-71513000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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