Variant report

Variant	rs12062719
Chromosome Location	chr1:151190100-151190101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151169634..151171700-chr1:151187471..151191348,3	MCF-7	breast:
2	chr1:151181898..151183969-chr1:151189213..151192203,2	MCF-7	breast:
3	1:151180715-151199990..1:151402394-151411623	GM12878	blood:
4	chr1:151168274..151172718-chr1:151186686..151190801,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238711	Chromatin interaction
ENSG00000143398	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10749660	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10788803	0.80[ASN][1000 genomes]
rs10888406	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888408	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204785	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11204791	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204795	0.85[ASN][1000 genomes]
rs11807075	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12022732	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12040384	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12048670	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12080778	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12407426	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16827941	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16833079	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892196	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275900	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41302131	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4291501	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4520422	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4970944	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4971013	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971015	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971016	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971021	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971023	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971025	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4971026	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4971027	0.83[ASN][1000 genomes]
rs58323986	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61817972	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587559	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587562	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6681071	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6681163	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6683396	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6686402	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695344	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6701325	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7521064	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7527032	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7532935	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7539584	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7544947	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151172800-151197200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:151172800-151204400	Weak transcription	Stomach Mucosa	stomach
3	chr1:151173200-151191600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:151173200-151196600	Weak transcription	K562	blood
5	chr1:151173200-151197000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:151173200-151199600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:151173200-151200000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:151173200-151212000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:151173200-151227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:151173600-151210600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:151174000-151194600	Weak transcription	Brain Substantia Nigra	brain
12	chr1:151174000-151199400	Weak transcription	Small Intestine	intestine
13	chr1:151174200-151200600	Weak transcription	Pancreas	Pancrea
14	chr1:151174400-151203800	Weak transcription	Fetal Brain Male	brain
15	chr1:151175800-151193800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:151175800-151199800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:151175800-151200400	Weak transcription	Aorta	Aorta
18	chr1:151176000-151194600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:151176200-151200400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:151176600-151196400	Weak transcription	Primary B cells from cord blood	blood
21	chr1:151176600-151197000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:151178200-151223400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:151179600-151197600	Weak transcription	Gastric	stomach
24	chr1:151180000-151193800	Weak transcription	Fetal Heart	heart
25	chr1:151180000-151196600	Weak transcription	Colonic Mucosa	Colon
26	chr1:151180200-151199800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:151180600-151198000	Weak transcription	Spleen	Spleen
28	chr1:151180800-151192800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:151180800-151194600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:151180800-151197200	Weak transcription	Ovary	ovary
31	chr1:151180800-151199800	Weak transcription	Esophagus	oesophagus
32	chr1:151180800-151206200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:151181000-151194600	Weak transcription	HSMMtube	muscle
34	chr1:151181200-151197200	Weak transcription	Right Ventricle	heart
35	chr1:151181200-151200200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:151181200-151203000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:151182400-151199600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:151182600-151196400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:151183400-151199800	Weak transcription	Brain Angular Gyrus	brain
40	chr1:151183600-151190400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:151183600-151193800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:151183600-151194400	Weak transcription	Adipose Nuclei	Adipose
43	chr1:151183600-151196200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:151183600-151197000	Weak transcription	Fetal Lung	lung
45	chr1:151183800-151190400	Weak transcription	NHLF	lung
46	chr1:151183800-151190600	Weak transcription	NHDF-Ad	bronchial
47	chr1:151183800-151192400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:151183800-151193400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:151183800-151193600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:151183800-151194600	Weak transcription	Liver	Liver

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