Variant report

Variant	rs16948241
Chromosome Location	chr12:118737072-118737073
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	chr12:118735634..118738198-chr12:118739744..118741334,2	K562	blood:
2	chr12:118734540..118737198-chr12:118753969..118757763,3	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10507286	0.83[LWK][hapmap];0.87[YRI][hapmap]
rs10507288	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[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	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs16948189	1.00[AMR][1000 genomes]
rs16948193	0.93[YRI][hapmap]
rs16948195	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948197	0.94[LWK][hapmap];0.87[YRI][hapmap]
rs16948199	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948204	0.94[LWK][hapmap];0.93[YRI][hapmap]
rs16948224	1.00[YRI][hapmap]
rs16948225	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948230	0.94[LWK][hapmap];0.93[YRI][hapmap]
rs16948234	0.94[LWK][hapmap];0.93[YRI][hapmap]
rs16948245	1.00[AMR][1000 genomes]
rs16948258	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948259	1.00[AMR][1000 genomes]
rs16948262	1.00[AMR][1000 genomes]
rs17433259	1.00[ASW][hapmap];0.92[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17440336	0.88[LWK][hapmap]
rs17440364	0.88[LWK][hapmap]
rs17512198	0.88[LWK][hapmap]
rs55965100	0.82[AFR][1000 genomes];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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57072278	1.00[AMR][1000 genomes]
rs57170485	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57865918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58340234	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58797246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59036425	1.00[AMR][1000 genomes]
rs59558138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60160994	1.00[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];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7963880	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7965350	0.93[YRI][hapmap]
rs7977168	1.00[AMR][1000 genomes]

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	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	nsv524938	chr12:118624736-118740675	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16948241	FHL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118673400-118737600	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:118673800-118737800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:118676000-118745200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:118677000-118739800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:118683400-118739800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:118693400-118745000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:118694600-118739800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:118699200-118737600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:118700200-118737200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:118700400-118738000	Weak transcription	Fetal Intestine Large	intestine
11	chr12:118702600-118744600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:118704000-118739000	Weak transcription	NHDF-Ad	bronchial
13	chr12:118709800-118737600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:118710800-118738000	Weak transcription	NHEK	skin
15	chr12:118712200-118739000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:118712400-118745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:118712600-118737400	Weak transcription	Small Intestine	intestine
18	chr12:118712800-118738000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:118715000-118741200	Weak transcription	Thymus	Thymus
20	chr12:118719200-118744400	Weak transcription	HSMM	muscle
21	chr12:118720800-118793600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:118721400-118739800	Weak transcription	Left Ventricle	heart
23	chr12:118721600-118739400	Weak transcription	Psoas Muscle	Psoas
24	chr12:118722400-118737800	Weak transcription	Fetal Lung	lung
25	chr12:118722600-118737800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:118722600-118739200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:118722600-118745000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:118726600-118746800	Weak transcription	Lung	lung
29	chr12:118728200-118739000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:118728400-118738000	Weak transcription	K562	blood
31	chr12:118728400-118744400	Weak transcription	NHLF	lung
32	chr12:118728600-118738000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:118731200-118744400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:118732600-118744800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:118732800-118767600	Weak transcription	Primary T cells from cord blood	blood
36	chr12:118733200-118738000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr12:118733400-118745000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:118733600-118737600	Weak transcription	GM12878-XiMat	blood
39	chr12:118735000-118744600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr12:118735200-118737800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:118735400-118737600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr12:118735400-118738800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:118735400-118744400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr12:118735600-118745000	Weak transcription	Primary B cells from cord blood	blood
45	chr12:118736200-118737800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:118736200-118746000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr12:118736400-118737600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:118736600-118737200	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr12:118736600-118737600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:118736600-118737600	Enhancers	Cortex derived primary cultured neurospheres	brain

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