Variant report

Variant	rs12924064
Chromosome Location	chr16:70805349-70805350
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:70556576..70558100-chr16:70803854..70806664,2	MCF-7	breast:
2	chr16:70778996..70782237-chr16:70803304..70807421,5	MCF-7	breast:
3	chr16:70772019..70772938-chr16:70804684..70805569,3	MCF-7	breast:
4	chr16:70771954..70772860-chr16:70804324..70805624,4	MCF-7	breast:
5	chr16:70718387..70720685-chr16:70803826..70806768,2	MCF-7	breast:
6	chr16:70690486..70692023-chr16:70804289..70805628,11	MCF-7	breast:
7	chr16:70711095..70714383-chr16:70803996..70807940,3	K562	blood:
8	chr16:70718298..70722651-chr16:70801198..70806372,7	MCF-7	breast:
9	chr16:70717721..70722436-chr16:70803445..70807809,5	K562	blood:
10	chr16:70690090..70691349-chr16:70804345..70805659,18	MCF-7	breast:
11	chr16:70802936..70806870-chr16:70807809..70811043,3	K562	blood:
12	chr16:70780643..70782977-chr16:70803241..70805880,2	MCF-7	breast:
13	chr16:70803133..70806870-chr16:70807809..70811183,4	K562	blood:
14	chr16:70690791..70691315-chr16:70804710..70805594,2	K562	blood:
15	chr16:70713636..70714554-chr16:70804662..70805566,3	MCF-7	breast:
16	chr16:70719951..70721525-chr16:70803849..70806342,2	K562	blood:
17	chr16:70687692..70688309-chr16:70805210..70805902,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL34-2	chr16:70802749-70807154	ENSG00000214353.3

No data

Variant related genes	Relation type
ENSG00000189091	Chromatin interaction
ENSG00000157368	Chromatin interaction
ENSG00000260156	Chromatin interaction
ENSG00000132613	Chromatin interaction
ENSG00000103051	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1009285	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11863319	0.87[ASN][1000 genomes]
rs11864614	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11866379	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12920588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12926985	0.89[ASN][1000 genomes]
rs12928270	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12929374	0.86[ASN][1000 genomes]
rs12934723	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12935645	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13335758	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1551528	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1551529	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970484	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16970513	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17248914	0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28676580	0.98[ASN][1000 genomes]
rs34268521	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35144432	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35426120	0.87[ASN][1000 genomes]
rs35665975	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3760118	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3855651	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985364	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4985425	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs52826576	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60190856	0.84[ASN][1000 genomes]
rs6416703	0.83[EUR][1000 genomes]
rs6499336	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs713511	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71384769	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71401831	0.87[ASN][1000 genomes]
rs7185921	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7188712	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7194091	0.82[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs7196225	0.93[ASN][1000 genomes]
rs7202363	0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs74024449	0.91[ASN][1000 genomes]
rs8044133	0.89[ASN][1000 genomes]
rs8052615	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs8060947	0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9931380	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517391	chr16:70666410-70840490	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv457517	chr16:70666722-70840490	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv572945	chr16:70666722-70840490	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1061191	chr16:70754975-71201367	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1059478	chr16:70773597-71237055	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70772600-70813400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr16:70773000-70805600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr16:70773000-70815800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr16:70773400-70816200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr16:70781200-70826800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr16:70781800-70815000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr16:70785000-70814200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr16:70785000-70814400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:70785000-70825000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr16:70785600-70813000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr16:70785800-70828000	Strong transcription	Primary T cells from cord blood	blood
12	chr16:70786600-70815200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr16:70786800-70815000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr16:70788000-70826600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr16:70789600-70810400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr16:70794600-70814200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr16:70794600-70816400	Weak transcription	Small Intestine	intestine
18	chr16:70795600-70808000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr16:70795600-70809200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr16:70795800-70814400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr16:70796000-70806800	Strong transcription	Fetal Intestine Small	intestine
22	chr16:70797000-70811200	Weak transcription	Right Ventricle	heart
23	chr16:70797000-70813000	Weak transcription	Fetal Kidney	kidney
24	chr16:70797800-70810200	Strong transcription	Fetal Intestine Large	intestine
25	chr16:70797800-70811400	Weak transcription	Left Ventricle	heart
26	chr16:70799200-70824000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr16:70799400-70809400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr16:70799800-70811200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr16:70800200-70805400	Genic enhancers	Fetal Muscle Leg	muscle
30	chr16:70800400-70809400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr16:70801800-70806000	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr16:70802000-70808600	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr16:70802200-70805400	Genic enhancers	Fetal Thymus	thymus
34	chr16:70802200-70805400	Genic enhancers	HSMM	muscle
35	chr16:70802200-70806200	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr16:70802400-70807000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr16:70802400-70808400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr16:70802400-70814400	Weak transcription	Stomach Mucosa	stomach
39	chr16:70802400-70825000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr16:70802600-70805600	Weak transcription	Psoas Muscle	Psoas
41	chr16:70802600-70806200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr16:70802800-70805800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr16:70802800-70810200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr16:70803000-70805400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr16:70803000-70806000	Strong transcription	Gastric	stomach
46	chr16:70803000-70808400	Strong transcription	Dnd41	blood
47	chr16:70803200-70805400	Strong transcription	Hela-S3	cervix
48	chr16:70803200-70806800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr16:70803200-70807200	Strong transcription	Adipose Nuclei	Adipose
50	chr16:70803200-70807200	Strong transcription	Rectal Mucosa Donor 29	rectum

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