Variant report

Variant	rs6539123
Chromosome Location	chr12:104461937-104461938
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104457600..104461691-chr12:104461792..104464629,3	K562	blood:
2	chr12:104457375..104460043-chr12:104460248..104462043,2	K562	blood:
3	chr12:104461547..104463720-chr12:104464282..104467136,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111727	Chromatin interaction
ENSG00000120820	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10861156	0.91[MKK][hapmap]
rs10861157	0.90[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11111888	0.90[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111892	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11111897	0.88[MKK][hapmap]
rs11111900	0.90[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12580532	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12580691	0.83[ASN][1000 genomes]
rs1485591	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]
rs2272477	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34011860	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34071758	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35223676	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35879815	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3763999	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4964531	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7133289	0.90[ASW][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7311508	0.81[MEX][hapmap]
rs7958015	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7979123	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[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
rs6539123	HCFC2	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104459200-104463600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:104459200-104480600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:104459200-104480600	Weak transcription	Esophagus	oesophagus
4	chr12:104459400-104464000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:104459400-104476600	Weak transcription	Fetal Kidney	kidney
6	chr12:104459600-104462800	Weak transcription	Primary B cells from cord blood	blood
7	chr12:104459600-104464000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr12:104459600-104476600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:104459600-104476600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:104459600-104481200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:104459800-104462400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:104459800-104463000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:104459800-104465000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:104459800-104465800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:104459800-104476600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:104459800-104476800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:104459800-104477400	Weak transcription	Gastric	stomach
18	chr12:104459800-104477600	Weak transcription	Small Intestine	intestine
19	chr12:104459800-104477800	Weak transcription	Spleen	Spleen
20	chr12:104459800-104491800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:104460000-104462200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:104460000-104462200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:104460000-104462400	Weak transcription	HUVEC	blood vessel
24	chr12:104460000-104463600	Weak transcription	Stomach Mucosa	stomach
25	chr12:104460000-104464800	Weak transcription	A549	lung
26	chr12:104460000-104464800	Weak transcription	HMEC	breast
27	chr12:104460000-104465000	Weak transcription	Ovary	ovary
28	chr12:104460000-104465000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:104460000-104465000	Weak transcription	GM12878-XiMat	blood
30	chr12:104460000-104468400	Strong transcription	Fetal Lung	lung
31	chr12:104460000-104476000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:104460000-104476600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:104460000-104476600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:104460000-104476600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:104460000-104476800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr12:104460000-104477600	Weak transcription	Aorta	Aorta
37	chr12:104460000-104482000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:104460000-104496800	Weak transcription	HepG2	liver
39	chr12:104460000-104511800	Weak transcription	Hela-S3	cervix
40	chr12:104460000-104526200	Weak transcription	Colonic Mucosa	Colon
41	chr12:104460200-104462200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:104460200-104462200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:104460200-104462400	Weak transcription	Brain Substantia Nigra	brain
44	chr12:104460200-104462400	Weak transcription	Thymus	Thymus
45	chr12:104460200-104463000	Weak transcription	Primary T cells from cord blood	blood
46	chr12:104460200-104463400	Weak transcription	NHLF	lung
47	chr12:104460200-104464800	Weak transcription	Brain Anterior Caudate	brain
48	chr12:104460200-104465000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:104460200-104468200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:104460200-104472600	Weak transcription	Fetal Heart	heart

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