Variant report

Variant	rs12598642
Chromosome Location	chr16:69848772-69848773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69838826..69841714-chr16:69847060..69849740,2	MCF-7	breast:
2	chr16:69830820..69833460-chr16:69847790..69850124,2	MCF-7	breast:
3	chr16:69848424..69850083-chr16:69853504..69855055,2	K562	blood:
4	chr16:69846629..69849489-chr16:70284143..70286922,2	K562	blood:

Variant related genes	Relation type
ENSG00000198373	Chromatin interaction
ENSG00000223496	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10852461	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs11075744	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[EUR][1000 genomes]
rs12446168	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12446197	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12919094	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12921407	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12925429	0.81[ASN][1000 genomes]
rs12926791	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12927052	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12927168	0.90[ASN][1000 genomes]
rs12927431	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1437134	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1466863	0.91[CHD][hapmap]
rs1500337	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1566453	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1566454	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1566455	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2102067	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2291959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2362641	0.87[EUR][1000 genomes]
rs2362642	0.93[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs244415	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs244417	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs244420	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs2937121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2937124	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3790075	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3790076	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3790078	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3790080	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3790083	1.00[CHD][hapmap]
rs4146819	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs4296254	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985448	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4985449	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4985450	0.91[CHD][hapmap]
rs6499240	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs6499244	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs6499263	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6499268	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6499269	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6499270	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs68161338	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7190013	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7192213	0.80[EUR][1000 genomes]
rs7193038	0.84[EUR][1000 genomes]
rs7196842	0.89[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7359336	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs8044876	0.88[EUR][1000 genomes]
rs8047682	0.87[EUR][1000 genomes]
rs8048550	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8049373	0.83[EUR][1000 genomes]
rs8050414	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8051168	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8052225	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8060478	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9940315	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69797600-69853400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:69807200-69852400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:69807200-69852800	Weak transcription	Hela-S3	cervix
4	chr16:69807200-69854800	Weak transcription	Psoas Muscle	Psoas
5	chr16:69817800-69854600	Weak transcription	HMEC	breast
6	chr16:69822400-69854800	Weak transcription	Stomach Mucosa	stomach
7	chr16:69823800-69874800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr16:69824200-69852400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr16:69830200-69856600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr16:69830600-69857600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr16:69830600-69864200	Weak transcription	Colon Smooth Muscle	Colon
12	chr16:69830600-69867000	Weak transcription	Right Ventricle	heart
13	chr16:69831000-69852400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr16:69831000-69852400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr16:69831000-69854800	Weak transcription	Aorta	Aorta
16	chr16:69831000-69856400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr16:69832400-69858400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr16:69833200-69854800	Weak transcription	NH-A	brain
19	chr16:69833400-69852400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr16:69833400-69854600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr16:69833400-69854600	Weak transcription	NHLF	lung
22	chr16:69833800-69854400	Weak transcription	Osteobl	bone
23	chr16:69833800-69854600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr16:69833800-69854800	Weak transcription	HSMM	muscle
25	chr16:69833800-69854800	Weak transcription	HSMMtube	muscle
26	chr16:69833800-69857600	Weak transcription	Small Intestine	intestine
27	chr16:69833800-69864400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr16:69833800-69874600	Weak transcription	Dnd41	blood
29	chr16:69833800-69875600	Weak transcription	NHEK	skin
30	chr16:69834000-69850400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr16:69834000-69852400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr16:69834000-69852400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr16:69834000-69852400	Weak transcription	Fetal Brain Female	brain
34	chr16:69834000-69854400	Weak transcription	Fetal Kidney	kidney
35	chr16:69834000-69855000	Weak transcription	Brain Germinal Matrix	brain
36	chr16:69834000-69910600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr16:69834200-69851600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr16:69834200-69851600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr16:69834200-69852400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr16:69834200-69857800	Weak transcription	Left Ventricle	heart
41	chr16:69834200-69892200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr16:69834400-69854800	Weak transcription	Brain Angular Gyrus	brain
43	chr16:69834400-69854800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr16:69835600-69852400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr16:69836400-69867400	Weak transcription	Colonic Mucosa	Colon
46	chr16:69836600-69852600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr16:69836800-69851400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr16:69836800-69864200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr16:69836800-69864400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr16:69837000-69905600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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