Variant report

Variant	rs12728967
Chromosome Location	chr1:78134934-78134935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78132958..78135412-chr1:78145762..78149652,4	MCF-7	breast:
2	chr1:78133704..78136431-chr1:78139980..78143480,5	K562	blood:
3	chr1:78134917..78136892-chr1:78138140..78140290,2	MCF-7	breast:
4	chr1:78134752..78136322-chr1:78136950..78139652,3	K562	blood:
5	chr1:78131407..78136393-chr1:78144019..78149939,7	K562	blood:
6	chr1:78127496..78129502-chr1:78132844..78136268,3	K562	blood:

Variant related genes	Relation type
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12402928	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12409142	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12741347	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12751064	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17381664	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1963170	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949660	1.00[ASN][1000 genomes]
rs4949662	1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6678622	1.00[JPT][hapmap];0.87[AMR][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	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78099000-78147200	Weak transcription	Gastric	stomach
2	chr1:78107600-78146000	Weak transcription	Fetal Kidney	kidney
3	chr1:78110400-78138000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:78111200-78147200	Weak transcription	Esophagus	oesophagus
5	chr1:78111400-78137400	Weak transcription	HUVEC	blood vessel
6	chr1:78111400-78137600	Weak transcription	Hela-S3	cervix
7	chr1:78112200-78139000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:78114800-78135000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:78114800-78135800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:78116800-78144600	Weak transcription	NHEK	skin
11	chr1:78117200-78144400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:78117400-78137200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:78117400-78138000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:78117400-78141800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:78117400-78147200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr1:78117600-78137400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:78117600-78137600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:78117600-78138200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:78117600-78139800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:78117600-78146000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:78117600-78147200	Weak transcription	Thymus	Thymus
22	chr1:78118200-78137200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:78118600-78146000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr1:78119000-78139000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:78119000-78145600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:78119000-78146000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:78119400-78147200	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:78120800-78147200	Weak transcription	Lung	lung
29	chr1:78121400-78137600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:78121400-78137600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:78121600-78137600	Weak transcription	A549	lung
32	chr1:78123800-78139400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:78124600-78146000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:78125800-78136000	Weak transcription	Spleen	Spleen
35	chr1:78127000-78135400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr1:78127000-78146400	Weak transcription	Primary B cells from cord blood	blood
37	chr1:78127400-78139800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:78128800-78137200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:78128800-78141000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:78128800-78141800	Weak transcription	Fetal Intestine Small	intestine
41	chr1:78131000-78141800	Weak transcription	Fetal Stomach	stomach
42	chr1:78131000-78146800	Weak transcription	Fetal Brain Female	brain
43	chr1:78131200-78135200	Enhancers	Fetal Lung	lung
44	chr1:78131200-78136000	Weak transcription	Brain Angular Gyrus	brain
45	chr1:78131200-78136400	Weak transcription	Brain Anterior Caudate	brain
46	chr1:78131200-78136400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:78131200-78136600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:78131200-78137200	Weak transcription	HSMMtube	muscle
49	chr1:78131200-78137400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:78131200-78137600	Weak transcription	HepG2	liver

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