Variant report

Variant	rs12121403
Chromosome Location	chr1:214807473-214807474
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:214774366..214777034-chr1:214805541..214808284,2	K562	blood:
2	chr1:214387373..214389349-chr1:214805200..214808187,2	MCF-7	breast:
3	chr1:214775592..214777676-chr1:214805586..214808335,2	MCF-7	breast:
4	chr1:214805392..214808282-chr1:214828137..214829833,2	K562	blood:
5	chr1:214800806..214805673-chr1:214807375..214811280,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117724	Chromatin interaction

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

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

rs_ID	r²[population]
rs12126024	0.91[CEU][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2070064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs335527	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs34721280	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35993967	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748697	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs374934	0.89[CEU][hapmap]
rs3795521	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390110	0.89[CEU][hapmap]
rs4311856	0.90[MEX][hapmap]

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	nsv1004475	chr1:214763778-215013375	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1005669	chr1:214774522-214994142	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv997864	chr1:214778658-214994142	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1002937	chr1:214793813-214994142	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1013284	chr1:214799847-214951184	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv873165	chr1:214802299-214889859	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214777600-214810800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:214777600-214838600	Weak transcription	Esophagus	oesophagus
3	chr1:214777800-214838400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:214778000-214839200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:214781200-214818000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:214783200-214817800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:214783400-214838800	Weak transcription	Fetal Kidney	kidney
8	chr1:214784600-214834000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:214785600-214819400	Strong transcription	K562	blood
10	chr1:214785600-214843800	Strong transcription	Fetal Thymus	thymus
11	chr1:214786200-214843000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:214786600-214833800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:214786600-214843200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:214786800-214843800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:214787600-214842200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:214788000-214810400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:214788200-214820600	Weak transcription	Fetal Heart	heart
18	chr1:214789000-214837400	Weak transcription	Small Intestine	intestine
19	chr1:214793600-214810400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:214793800-214810200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:214794400-214833200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:214795200-214838600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:214795600-214807600	Weak transcription	Primary B cells from cord blood	blood
24	chr1:214801000-214812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:214801000-214839600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:214801000-214843000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:214801200-214846000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:214801600-214811000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:214801600-214811000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:214801800-214816400	Strong transcription	Hela-S3	cervix
31	chr1:214801800-214841400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:214801800-214842600	Strong transcription	A549	lung
33	chr1:214801800-214844800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr1:214802000-214807800	Strong transcription	HUVEC	blood vessel
35	chr1:214802000-214808000	Strong transcription	HMEC	breast
36	chr1:214802000-214808400	Strong transcription	Osteobl	bone
37	chr1:214802000-214809000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:214802000-214820400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:214802000-214842000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:214802400-214841600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:214802600-214810600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:214803000-214808800	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr1:214803000-214809000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:214803200-214808800	Strong transcription	Primary hematopoietic stem cells	blood
45	chr1:214803200-214808800	Strong transcription	Fetal Stomach	stomach
46	chr1:214803200-214809000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:214803200-214809800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr1:214803200-214810000	Strong transcription	HepG2	liver
49	chr1:214803200-214810600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:214803200-214820000	Strong transcription	GM12878-XiMat	blood

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