Variant report

Variant	rs11052015
Chromosome Location	chr12:32624276-32624277
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BICD1-3	chr12:32624229-32624656	NONHSAT027612

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11052012	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11052014	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367135	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1566513	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566514	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047643	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2388991	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34382604	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34957239	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61927222	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[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	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv898970	chr12:32622097-32680236	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32594600-32659000	Weak transcription	Esophagus	oesophagus
2	chr12:32601800-32629400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:32602600-32636400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:32606000-32624600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:32606000-32624600	Weak transcription	Gastric	stomach
6	chr12:32606600-32624600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:32608600-32629600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:32610400-32628400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:32610800-32624400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:32610800-32636400	Weak transcription	NHEK	skin
11	chr12:32610800-32639000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:32611200-32629000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:32616000-32638600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:32616600-32628200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:32616800-32624400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:32617000-32629000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:32617000-32629200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:32619200-32627000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:32619400-32626200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:32619400-32627600	Weak transcription	Fetal Stomach	stomach
21	chr12:32619600-32642000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:32620800-32627800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:32621000-32624600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:32621400-32624400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:32621400-32629400	Weak transcription	Adipose Nuclei	Adipose
26	chr12:32621600-32624400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:32621600-32624600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:32621600-32626600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr12:32621600-32630400	Weak transcription	Fetal Kidney	kidney
30	chr12:32621600-32631200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:32621600-32636400	Weak transcription	Right Ventricle	heart
32	chr12:32621800-32628600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:32621800-32630600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:32621800-32631200	Weak transcription	HUVEC	blood vessel
35	chr12:32621800-32654000	Weak transcription	Lung	lung
36	chr12:32622000-32624600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:32622000-32631200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:32622200-32630400	Weak transcription	Primary B cells from cord blood	blood
39	chr12:32623000-32625200	Genic enhancers	Fetal Intestine Small	intestine
40	chr12:32623200-32624800	Enhancers	Psoas Muscle	Psoas
41	chr12:32623200-32625000	Enhancers	Fetal Intestine Large	intestine
42	chr12:32623200-32627200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:32623400-32624600	Weak transcription	HSMM	muscle
44	chr12:32623400-32624800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:32623400-32625800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:32623600-32624800	Strong transcription	HMEC	breast
47	chr12:32623600-32625000	Enhancers	Liver	Liver
48	chr12:32623600-32625000	Enhancers	Ovary	ovary
49	chr12:32623600-32625200	Enhancers	Pancreas	Pancrea
50	chr12:32623800-32625000	Enhancers	Duodenum Mucosa	Duodenum

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