Variant report

Variant	rs2641468
Chromosome Location	chr12:74937958-74937959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:74934002..74935915-chr12:74937667..74942932,5	K562	blood:
2	chr12:74937896..74940364-chr12:74944289..74945994,2	K562	blood:
3	chr12:74936725..74942637-chr12:74943509..74950364,10	MCF-7	breast:
4	chr12:74936849..74938851-chr12:74961642..74963364,2	MCF-7	breast:
5	chr12:74933499..74938752-chr12:74938991..74943644,10	K562	blood:
6	chr12:74920482..74922543-chr12:74935619..74938584,2	MCF-7	breast:
7	chr12:74929601..74933992-chr12:74933997..74938801,8	K562	blood:

Variant related genes	Relation type
ENSG00000257386	Chromatin interaction
ENSG00000253719	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11180097	0.83[AFR][1000 genomes]
rs12816388	0.95[CHB][hapmap];0.96[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1389492	0.80[ASN][1000 genomes]
rs1493797	0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs1493805	0.81[ASN][1000 genomes]
rs1493806	0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2605338	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2605374	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2605376	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605377	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2613882	0.90[CHB][hapmap]
rs2613887	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2613895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2613900	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2613901	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2613903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2641467	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2641481	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4882641	0.82[ASN][1000 genomes]
rs4882642	0.82[ASN][1000 genomes]
rs597888	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs628576	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs647129	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8744	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv899293	chr12:74835107-74995760	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv899295	chr12:74854750-74984992	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv470303	chr12:74880668-74945356	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	n/a
5	nsv899296	chr12:74880668-74974630	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74933800-74942800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:74934200-74942000	Weak transcription	Ovary	ovary
3	chr12:74934400-74938400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:74934600-74940800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:74935200-74938200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:74935200-74940800	Weak transcription	Pancreas	Pancrea
7	chr12:74935200-74941000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:74935200-74941800	Weak transcription	Thymus	Thymus
9	chr12:74935200-74942200	Weak transcription	Psoas Muscle	Psoas
10	chr12:74935200-74942600	Weak transcription	Small Intestine	intestine
11	chr12:74935200-74943600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:74935200-74945000	Weak transcription	Left Ventricle	heart
13	chr12:74935400-74942600	Weak transcription	Fetal Intestine Small	intestine
14	chr12:74935600-74938000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:74935600-74939000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:74935600-74941000	Weak transcription	Fetal Stomach	stomach
17	chr12:74935600-74941400	Weak transcription	Adipose Nuclei	Adipose
18	chr12:74935600-74942000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:74935600-74942400	Weak transcription	NHDF-Ad	bronchial
20	chr12:74935600-74943200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:74935800-74939400	Weak transcription	A549	lung
22	chr12:74935800-74940400	Weak transcription	Hela-S3	cervix
23	chr12:74935800-74941000	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:74935800-74942800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:74936000-74938400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:74936000-74942200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr12:74936000-74942400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:74936000-74942600	Weak transcription	Fetal Intestine Large	intestine
29	chr12:74936000-74945600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:74936200-74939800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr12:74936200-74940000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:74936200-74940200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr12:74936200-74940800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:74936200-74941200	Weak transcription	Fetal Thymus	thymus
35	chr12:74936200-74942600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:74936200-74943600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:74936400-74938000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:74936400-74938000	Weak transcription	HepG2	liver
39	chr12:74936400-74938000	Weak transcription	NHEK	skin
40	chr12:74936400-74938600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr12:74936400-74939200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:74936400-74939400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:74936400-74942000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:74936400-74945000	Weak transcription	Fetal Heart	heart
45	chr12:74936600-74938200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:74936600-74941000	Weak transcription	Dnd41	blood
47	chr12:74936600-74942400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:74936800-74938400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr12:74936800-74942000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:74936800-74942600	Weak transcription	Liver	Liver

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