Variant report

Variant	rs1880886
Chromosome Location	chr12:41728175-41728176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:41726380..41728988-chr12:41729425..41732351,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10735992	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10785246	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10785251	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10785253	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10785257	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs10880041	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs10880060	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11180878	0.92[YRI][hapmap]
rs1358272	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1458176	0.92[YRI][hapmap]
rs1527088	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs17129253	0.88[ASN][1000 genomes]
rs1997192	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049592	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs2141108	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs2177976	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2199030	0.92[YRI][hapmap]
rs2405912	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs4447233	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768351	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7133896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7134525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73124826	0.97[ASN][1000 genomes]
rs7954106	0.92[YRI][hapmap]
rs7957823	0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv832383	chr12:41693298-41846934	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41721200-41729600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:41722800-41733000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:41723200-41731200	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:41726000-41728600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr12:41726600-41728800	Enhancers	Brain Germinal Matrix	brain
6	chr12:41726800-41730400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:41727000-41728600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:41727000-41730200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:41727000-41730600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:41727000-41730600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr12:41727200-41728400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:41727200-41728600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr12:41727200-41728600	Enhancers	Brain Substantia Nigra	brain
14	chr12:41727200-41728800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr12:41727400-41728600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:41727400-41728600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr12:41727600-41728400	Enhancers	Fetal Brain Female	brain
18	chr12:41727600-41730400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr12:41727600-41730400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:41727800-41728600	Enhancers	H9 Cell Line	embryonic stem cell
21	chr12:41727800-41728600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:41727800-41728600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:41727800-41730200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:41728000-41728200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr12:41728000-41728800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr12:41728000-41730400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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