Variant report

Variant	rs12228948
Chromosome Location	chr12:105567825-105567826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105559645..105562741-chr12:105564536..105567836,4	K562	blood:
2	chr12:105564992..105569001-chr12:105627432..105630831,3	K562	blood:
3	chr12:105564104..105568210-chr12:105569076..105573485,6	MCF-7	breast:
4	chr12:105561858..105564430-chr12:105566394..105568503,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1014502	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10431460	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1057110	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1077896	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861359	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861361	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1109433	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112369	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112370	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112372	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112375	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112376	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112379	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112388	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112409	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112412	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112415	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11112416	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11112421	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112423	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112432	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11831854	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11832489	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834277	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12228093	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12230762	0.82[ASN][1000 genomes]
rs12812433	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12815031	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12819309	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12830078	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317955	0.90[EUR][1000 genomes]
rs1373552	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1444611	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1470381	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2272495	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293643	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2293644	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2464176	0.93[ASN][1000 genomes]
rs28549976	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34075890	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34119882	0.80[ASN][1000 genomes]
rs34983773	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35462155	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35672903	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736628	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794222	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3794223	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3794224	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3794227	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3817607	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829296	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4964125	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4964334	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4964335	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964336	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964338	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964339	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4964340	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4964342	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55908437	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56693261	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179994	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7485364	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755604	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8015	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881279	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9919746	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	esv1826054	chr12:105505809-105568176	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv870352	chr12:105557770-105589263	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105505200-105573000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr12:105505600-105573200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:105505800-105571400	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr12:105506400-105573000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:105506800-105568800	Strong transcription	Dnd41	blood
6	chr12:105506800-105572400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr12:105507000-105573200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:105507200-105571400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr12:105507600-105571400	Strong transcription	HUVEC	blood vessel
10	chr12:105507600-105572800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:105507800-105573200	Strong transcription	Placenta	Placenta
12	chr12:105508200-105572800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:105508600-105573000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:105518600-105573200	Strong transcription	HSMM	muscle
15	chr12:105522600-105586000	Weak transcription	Stomach Mucosa	stomach
16	chr12:105524600-105578200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:105525400-105583200	Weak transcription	Fetal Heart	heart
18	chr12:105529800-105571400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:105532400-105577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:105555200-105573200	Strong transcription	A549	lung
22	chr12:105556200-105583400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:105557400-105571600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:105557600-105578000	Weak transcription	Gastric	stomach
25	chr12:105558200-105578200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:105558200-105578400	Weak transcription	Right Ventricle	heart
27	chr12:105558200-105587200	Weak transcription	Psoas Muscle	Psoas
28	chr12:105558400-105578000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr12:105559000-105569000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:105559400-105578800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:105560400-105568000	Weak transcription	Fetal Stomach	stomach
33	chr12:105560800-105581800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:105561000-105572600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:105561400-105569200	Weak transcription	Fetal Brain Female	brain
36	chr12:105561400-105598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:105561600-105572800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:105561600-105572800	Strong transcription	NHDF-Ad	bronchial
39	chr12:105561600-105573600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:105561800-105573200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:105562000-105568000	Weak transcription	NHEK	skin
42	chr12:105562400-105571600	Strong transcription	Fetal Intestine Large	intestine
43	chr12:105563000-105571400	Strong transcription	Fetal Thymus	thymus
44	chr12:105563000-105573400	Strong transcription	Primary B cells from cord blood	blood
45	chr12:105563200-105572000	Strong transcription	Primary T cells from cord blood	blood
46	chr12:105563200-105573200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:105563400-105571400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr12:105563600-105568400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:105563600-105569000	Weak transcription	Hela-S3	cervix
50	chr12:105563800-105568000	Weak transcription	Rectal Smooth Muscle	rectum

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