Variant report

Variant	rs11171677
Chromosome Location	chr12:56177954-56177955
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56177105..56179829-chr12:56184444..56185951,2	K562	blood:
2	chr12:56176335..56178983-chr12:56210531..56213232,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123353	Chromatin interaction
ENSG00000205323	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10082864	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10083186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10161417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171667	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[EUR][1000 genomes]
rs11171670	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11171671	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11171681	0.91[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11829536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs11834264	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12304296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12304507	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12320756	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17117974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291267	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[ASN][1000 genomes]
rs3759101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7297523	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7299222	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7971247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7972345	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs868051	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56142000-56191800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56144600-56208800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:56144800-56198600	Strong transcription	Primary B cells from peripheral blood	blood
4	chr12:56145200-56199400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:56149400-56209600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:56152600-56179600	Weak transcription	Pancreas	Pancrea
7	chr12:56152800-56209000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:56153000-56182400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:56154400-56178400	Weak transcription	Fetal Brain Male	brain
10	chr12:56154400-56180600	Weak transcription	Right Ventricle	heart
11	chr12:56160000-56179600	Weak transcription	Aorta	Aorta
12	chr12:56160000-56197600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:56160200-56180000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:56160200-56184600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:56160400-56209600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:56162200-56183200	Strong transcription	Primary T cells from cord blood	blood
17	chr12:56163000-56198600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:56163200-56199800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:56163200-56209400	Strong transcription	Fetal Thymus	thymus
20	chr12:56163400-56184600	Strong transcription	Placenta	Placenta
21	chr12:56163400-56198000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:56164000-56197600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:56164200-56178200	Strong transcription	Fetal Stomach	stomach
24	chr12:56164800-56185000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:56166000-56178000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:56166400-56182000	Weak transcription	Small Intestine	intestine
27	chr12:56166400-56182600	Weak transcription	Fetal Heart	heart
28	chr12:56166400-56194600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:56169200-56195400	Strong transcription	Primary B cells from cord blood	blood
30	chr12:56169200-56197600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:56169400-56198400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:56169400-56198600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:56169400-56198600	Strong transcription	Dnd41	blood
34	chr12:56169600-56178200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:56169600-56185000	Strong transcription	Adipose Nuclei	Adipose
36	chr12:56169600-56185000	Strong transcription	HSMM	muscle
37	chr12:56169600-56185200	Strong transcription	K562	blood
38	chr12:56169600-56198200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr12:56169600-56198200	Strong transcription	Liver	Liver
40	chr12:56169800-56185000	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr12:56169800-56197600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr12:56169800-56203400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:56169800-56204200	Strong transcription	Fetal Muscle Leg	muscle
44	chr12:56170000-56185200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:56170000-56190800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:56170000-56197400	Strong transcription	Duodenum Mucosa	Duodenum
47	chr12:56170000-56197800	Strong transcription	Fetal Intestine Large	intestine
48	chr12:56170000-56198800	Strong transcription	HUVEC	blood vessel
49	chr12:56170200-56197400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr12:56170200-56198800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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