Variant report

Variant	rs7954839
Chromosome Location	chr12:56201191-56201192
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	chr12:56194831..56201406-chr12:56201561..56204912,5	K562	blood:
2	chr12:56199186..56201300-chr12:56209589..56212662,3	K562	blood:

Variant related genes	Relation type
ENSG00000205323	Chromatin interaction
ENSG00000123353	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1081732	0.86[AMR][1000 genomes]
rs10876851	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876852	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10876854	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11171681	0.91[CHB][hapmap]
rs11829536	0.90[JPT][hapmap]
rs12372076	0.92[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1681087	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291268	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2694012	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2887998	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs7305787	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs772262	0.93[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs772263	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7954619	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7965333	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56144600-56208800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:56149400-56209600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56152800-56209000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:56160400-56209600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:56163200-56209400	Strong transcription	Fetal Thymus	thymus
6	chr12:56169800-56203400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:56169800-56204200	Strong transcription	Fetal Muscle Leg	muscle
8	chr12:56170200-56204200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:56175200-56204200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:56178800-56209200	Weak transcription	Stomach Mucosa	stomach
11	chr12:56183200-56202200	Weak transcription	Small Intestine	intestine
12	chr12:56183200-56202400	Weak transcription	Pancreas	Pancrea
13	chr12:56183400-56210600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:56184800-56207800	Weak transcription	Fetal Heart	heart
15	chr12:56185000-56209400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:56187400-56202000	Weak transcription	Right Ventricle	heart
17	chr12:56187400-56208400	Weak transcription	Psoas Muscle	Psoas
18	chr12:56189200-56202400	Weak transcription	Ovary	ovary
19	chr12:56189600-56207600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:56189800-56208000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:56189800-56208800	Weak transcription	Fetal Brain Male	brain
22	chr12:56189800-56209600	Weak transcription	Brain Substantia Nigra	brain
23	chr12:56191000-56202400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:56193200-56206400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:56193200-56207800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:56193200-56209200	Weak transcription	Colonic Mucosa	Colon
27	chr12:56194600-56202800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:56195000-56209000	Weak transcription	HSMMtube	muscle
29	chr12:56195200-56202200	Weak transcription	Brain Angular Gyrus	brain
30	chr12:56195400-56202800	Weak transcription	Primary B cells from cord blood	blood
31	chr12:56195400-56205000	Weak transcription	NHLF	lung
32	chr12:56195600-56202000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr12:56195600-56202200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:56195600-56206200	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:56195600-56209200	Weak transcription	Spleen	Spleen
36	chr12:56195600-56210600	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:56195800-56202400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:56195800-56202400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:56195800-56203000	Weak transcription	Gastric	stomach
40	chr12:56195800-56203000	Weak transcription	HepG2	liver
41	chr12:56195800-56209200	Weak transcription	Brain Anterior Caudate	brain
42	chr12:56195800-56209600	Weak transcription	Fetal Kidney	kidney
43	chr12:56195800-56210200	Weak transcription	Aorta	Aorta
44	chr12:56196000-56202400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:56196000-56202400	Weak transcription	K562	blood
46	chr12:56196000-56205600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:56196000-56207800	Weak transcription	NHDF-Ad	bronchial
48	chr12:56196200-56206400	Weak transcription	NH-A	brain
49	chr12:56196800-56202600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:56196800-56202800	Weak transcription	NHEK	skin

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