Variant report

Variant	rs16948258
Chromosome Location	chr12:118784529-118784530
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118783117..118785703-chr12:118815737..118817299,2	K562	blood:
2	chr12:118779295..118781824-chr12:118782291..118786005,4	K562	blood:
3	chr12:118777906..118781488-chr12:118782215..118786255,6	K562	blood:
4	chr12:118778728..118784992-chr12:118810812..118815576,8	K562	blood:

Variant related genes	Relation type
ENSG00000270482	Chromatin interaction
ENSG00000111707	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10507286	0.87[YRI][hapmap]
rs10507288	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948163	1.00[AMR][1000 genomes]
rs16948168	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs16948171	1.00[AMR][1000 genomes]
rs16948173	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs16948189	1.00[AMR][1000 genomes]
rs16948193	0.93[YRI][hapmap]
rs16948195	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948197	0.87[YRI][hapmap]
rs16948199	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948204	0.93[YRI][hapmap]
rs16948224	1.00[YRI][hapmap]
rs16948225	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948230	0.93[YRI][hapmap]
rs16948234	0.93[YRI][hapmap]
rs16948241	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948245	1.00[AMR][1000 genomes]
rs16948259	1.00[AMR][1000 genomes]
rs16948262	1.00[AMR][1000 genomes]
rs17433259	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55965100	1.00[AMR][1000 genomes]
rs56210304	1.00[AMR][1000 genomes]
rs56319724	1.00[AMR][1000 genomes]
rs56743940	1.00[AMR][1000 genomes]
rs56802741	1.00[AMR][1000 genomes]
rs56819745	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57170485	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57865918	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58340234	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58797246	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59036425	1.00[AMR][1000 genomes]
rs59558138	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60160994	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60749048	1.00[AMR][1000 genomes]
rs60917706	1.00[AMR][1000 genomes]
rs7303417	0.93[YRI][hapmap]
rs7962185	0.93[YRI][hapmap]
rs7963735	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7963880	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7965350	0.93[YRI][hapmap]
rs7977168	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1038224	chr12:118648415-118791388	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1040061	chr12:118648415-118800437	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1053417	chr12:118688969-118808530	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr12:118720800-118793600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:118746200-118785000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:118768800-118790400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:118769200-118785000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:118769200-118785800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:118769200-118791000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:118770000-118785200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:118774000-118792400	Weak transcription	Dnd41	blood
9	chr12:118775800-118792000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:118775800-118792600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:118776200-118792000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:118777000-118791000	Weak transcription	NHDF-Ad	bronchial
13	chr12:118777200-118784800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:118780000-118790400	Weak transcription	Liver	Liver
15	chr12:118780200-118784600	Weak transcription	Brain Angular Gyrus	brain
16	chr12:118780200-118784800	Weak transcription	Stomach Mucosa	stomach
17	chr12:118780400-118785600	Weak transcription	A549	lung
18	chr12:118780800-118784800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:118781000-118793600	Weak transcription	NHEK	skin
20	chr12:118781800-118785200	Enhancers	Primary hematopoietic stem cells	blood
21	chr12:118782000-118785600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr12:118782000-118786600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr12:118782200-118786000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr12:118782600-118785600	Enhancers	Primary B cells from cord blood	blood
25	chr12:118782800-118784800	Weak transcription	Left Ventricle	heart
26	chr12:118782800-118786000	Enhancers	Brain Substantia Nigra	brain
27	chr12:118783200-118785000	Enhancers	Fetal Lung	lung
28	chr12:118783200-118786200	Enhancers	Brain Anterior Caudate	brain
29	chr12:118783400-118784800	Weak transcription	Small Intestine	intestine
30	chr12:118783400-118785000	Weak transcription	Fetal Intestine Small	intestine
31	chr12:118783400-118785800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr12:118783400-118789400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:118783400-118791000	Weak transcription	NHLF	lung
34	chr12:118783600-118784800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:118783600-118784800	Weak transcription	Psoas Muscle	Psoas
36	chr12:118783600-118785000	Weak transcription	Gastric	stomach
37	chr12:118783600-118785400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:118783600-118785800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:118783600-118792200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:118783600-118793000	Weak transcription	Osteobl	bone
41	chr12:118783600-118794400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr12:118783800-118784800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:118783800-118784800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:118784000-118786200	Enhancers	Duodenum Mucosa	Duodenum
45	chr12:118784200-118784800	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr12:118784200-118785000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:118784200-118786000	Enhancers	Brain Cingulate Gyrus	brain
48	chr12:118784200-118786200	Enhancers	Primary B cells from peripheral blood	blood
49	chr12:118784200-118793600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:118784400-118784800	Flanking Active TSS	K562	blood

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