Variant report

Variant	rs7966919
Chromosome Location	chr12:32624462-32624463
allele	C/T
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: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10743792	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743793	0.99[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771950	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10771951	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10771952	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10771953	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10771954	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10844208	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844209	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10844210	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2728715	0.89[CEU][hapmap]
rs4931631	0.80[AFR][1000 genomes]
rs58048246	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58632707	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488058	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7138653	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297833	0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7309641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309975	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310262	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310497	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312483	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7312780	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7314407	0.99[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954700	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954906	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954974	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7962302	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969497	0.80[AFR][1000 genomes]
rs7971819	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7977859	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979525	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	chr12:32610800-32636400	Weak transcription	NHEK	skin
10	chr12:32610800-32639000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:32611200-32629000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:32616000-32638600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:32616600-32628200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:32617000-32629000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:32617000-32629200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:32619200-32627000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:32619400-32626200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:32619400-32627600	Weak transcription	Fetal Stomach	stomach
19	chr12:32619600-32642000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:32620800-32627800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:32621000-32624600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:32621400-32629400	Weak transcription	Adipose Nuclei	Adipose
23	chr12:32621600-32624600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:32621600-32626600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:32621600-32630400	Weak transcription	Fetal Kidney	kidney
26	chr12:32621600-32631200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:32621600-32636400	Weak transcription	Right Ventricle	heart
28	chr12:32621800-32628600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:32621800-32630600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:32621800-32631200	Weak transcription	HUVEC	blood vessel
31	chr12:32621800-32654000	Weak transcription	Lung	lung
32	chr12:32622000-32624600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:32622000-32631200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:32622200-32630400	Weak transcription	Primary B cells from cord blood	blood
35	chr12:32623000-32625200	Genic enhancers	Fetal Intestine Small	intestine
36	chr12:32623200-32624800	Enhancers	Psoas Muscle	Psoas
37	chr12:32623200-32625000	Enhancers	Fetal Intestine Large	intestine
38	chr12:32623200-32627200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:32623400-32624600	Weak transcription	HSMM	muscle
40	chr12:32623400-32624800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:32623400-32625800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:32623600-32624800	Strong transcription	HMEC	breast
43	chr12:32623600-32625000	Enhancers	Liver	Liver
44	chr12:32623600-32625000	Enhancers	Ovary	ovary
45	chr12:32623600-32625200	Enhancers	Pancreas	Pancrea
46	chr12:32623800-32625000	Enhancers	Duodenum Mucosa	Duodenum
47	chr12:32624000-32624800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:32624000-32625000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:32624000-32625200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:32624200-32624600	Weak transcription	Left Ventricle	heart

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