Variant report

Variant	rs1485591
Chromosome Location	chr12:104500906-104500907
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	chr12:104457709..104459899-chr12:104500671..104502291,2	K562	blood:
2	chr12:104499633..104501724-chr12:104506063..104508976,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111727	Chromatin interaction
ENSG00000120820	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10861157	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111888	0.90[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11111892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111897	0.81[MKK][hapmap]
rs11111900	0.90[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12580532	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12580691	0.99[ASN][1000 genomes]
rs2272477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34011860	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34071758	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35223676	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35879815	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3763999	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964531	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539123	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7133289	0.90[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311508	0.81[MEX][hapmap]
rs7958015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7979123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1485591	HCFC2	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104460000-104511800	Weak transcription	Hela-S3	cervix
2	chr12:104460000-104526200	Weak transcription	Colonic Mucosa	Colon
3	chr12:104472400-104501200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:104477200-104508400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:104480000-104508400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:104482800-104508200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:104486200-104503000	Weak transcription	Small Intestine	intestine
8	chr12:104489200-104502600	Weak transcription	Psoas Muscle	Psoas
9	chr12:104491000-104508600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:104492000-104512400	Weak transcription	HMEC	breast
11	chr12:104493200-104502200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:104493200-104512400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:104493200-104514400	Weak transcription	NHEK	skin
14	chr12:104493400-104502400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:104493400-104502600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:104493400-104502600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:104493400-104502600	Weak transcription	Dnd41	blood
18	chr12:104493400-104502800	Weak transcription	A549	lung
19	chr12:104493400-104511800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:104493400-104513400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:104493400-104514400	Weak transcription	Brain Substantia Nigra	brain
22	chr12:104493400-104519200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:104493400-104519800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:104493600-104502600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:104493600-104505000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:104493600-104510800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:104493600-104517400	Weak transcription	Right Ventricle	heart
28	chr12:104493800-104515400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:104493800-104518400	Weak transcription	Gastric	stomach
30	chr12:104493800-104530600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:104494200-104502600	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:104494200-104502800	Weak transcription	Brain Anterior Caudate	brain
33	chr12:104494200-104509200	Weak transcription	Fetal Brain Male	brain
34	chr12:104494400-104502600	Weak transcription	Thymus	Thymus
35	chr12:104494400-104508000	Weak transcription	GM12878-XiMat	blood
36	chr12:104494400-104513600	Weak transcription	Brain Germinal Matrix	brain
37	chr12:104494400-104514000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:104494400-104516200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:104494400-104516200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:104494400-104521000	Weak transcription	Lung	lung
41	chr12:104494400-104521200	Weak transcription	Aorta	Aorta
42	chr12:104494400-104522600	Weak transcription	Spleen	Spleen
43	chr12:104494600-104516000	Weak transcription	Fetal Stomach	stomach
44	chr12:104494800-104505000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:104494800-104508400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:104494800-104509000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:104494800-104509200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:104495000-104502800	Weak transcription	Osteobl	bone
49	chr12:104495400-104506400	Weak transcription	Fetal Intestine Small	intestine
50	chr12:104495600-104508400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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