Variant report

Variant	rs12525400
Chromosome Location	chr6:29572160-29572161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29567658..29569553-chr6:29570192..29572225,2	K562	blood:
2	chr6:29571256..29575251-chr6:29575309..29583536,9	K562	blood:
3	chr6:29564780..29575712-chr6:29592511..29597522,14	K562	blood:
4	chr6:29566358..29568865-chr6:29570413..29572313,3	K562	blood:
5	chr6:29566782..29572750-chr6:29592808..29598864,8	K562	blood:

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12524535	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12528017	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12530421	0.83[EUR][1000 genomes]
rs17178028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267635	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28893512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28893514	0.86[EUR][1000 genomes]
rs28893515	0.86[EUR][1000 genomes]
rs28893516	0.86[EUR][1000 genomes]
rs28893517	0.86[EUR][1000 genomes]
rs28986291	0.90[AMR][1000 genomes]
rs28986295	0.86[EUR][1000 genomes]
rs28986296	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28986297	0.83[EUR][1000 genomes]
rs28986298	0.83[EUR][1000 genomes]
rs28986299	0.92[EUR][1000 genomes]
rs28986300	0.81[EUR][1000 genomes]
rs28986301	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28986303	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28986306	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28986307	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28986308	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29242	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3025645	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3025646	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3025649	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs362521	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3828923	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41286283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41286287	0.84[EUR][1000 genomes]
rs41291762	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41291766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs715044	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv528285	chr6:29566842-29588146	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv462671	chr6:29566842-29588146	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv601229	chr6:29566842-29588146	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv526617	chr6:29571545-29576393	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29561800-29573200	Weak transcription	HSMMtube	muscle
2	chr6:29562000-29572600	Weak transcription	Fetal Heart	heart
3	chr6:29565600-29572200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr6:29566400-29595200	Weak transcription	Right Atrium	heart
5	chr6:29566600-29587000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr6:29566800-29572400	Weak transcription	HUVEC	blood vessel
7	chr6:29566800-29584600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:29566800-29590000	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr6:29566800-29590600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:29567000-29589800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:29567200-29589400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:29567200-29589800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:29567600-29574600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:29567600-29583800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:29567600-29592400	Strong transcription	Fetal Stomach	stomach
16	chr6:29567600-29595400	Weak transcription	A549	lung
17	chr6:29567800-29582800	Strong transcription	Ovary	ovary
18	chr6:29567800-29584600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:29568000-29572200	Weak transcription	Primary T cells from cord blood	blood
20	chr6:29568000-29574600	Weak transcription	HSMM	muscle
21	chr6:29568200-29572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:29568400-29572400	Weak transcription	Dnd41	blood
23	chr6:29568400-29582600	Strong transcription	HMEC	breast
24	chr6:29568400-29583600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:29568600-29595200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:29568800-29572200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:29568800-29578000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:29568800-29583200	Strong transcription	NHEK	skin
29	chr6:29569000-29582600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr6:29569000-29582800	Strong transcription	Osteobl	bone
31	chr6:29569000-29584600	Strong transcription	Spleen	Spleen
32	chr6:29569000-29592400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:29569200-29572200	Weak transcription	Fetal Intestine Small	intestine
34	chr6:29569200-29572600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr6:29569200-29582800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:29569200-29592200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:29569400-29572200	Strong transcription	Fetal Muscle Leg	muscle
38	chr6:29569400-29581600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:29569400-29581600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:29569400-29582400	Strong transcription	Fetal Lung	lung
41	chr6:29569400-29592000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr6:29569400-29595600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:29569600-29581800	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr6:29569600-29582400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:29569800-29583000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:29569800-29583200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr6:29570000-29572800	Strong transcription	Brain Hippocampus Middle	brain
48	chr6:29570000-29573200	Strong transcription	Brain Substantia Nigra	brain
49	chr6:29570000-29576200	Strong transcription	Rectal Smooth Muscle	rectum
50	chr6:29570000-29577400	Strong transcription	NHLF	lung

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