Variant report

Variant	rs12721427
Chromosome Location	chr12:48368541-48368542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48366900..48369507-chr12:48392554..48394762,2	MCF-7	breast:
2	chr12:48366898..48369197-chr12:48592697..48594577,2	K562	blood:
3	chr12:48365132..48368005-chr12:48368353..48370036,2	K562	blood:
4	chr12:48366493..48369414-chr12:48372046..48373592,2	K562	blood:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10219510	0.84[CEU][hapmap]
rs11168244	1.00[LWK][hapmap]
rs11168331	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11503871	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11503873	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12300271	1.00[GIH][hapmap]
rs12313208	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12721425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12721426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541408	1.00[ASW][hapmap];0.92[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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17607800	1.00[ASW][hapmap]
rs17801742	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs2408878	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35000511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077869	1.00[CHB][hapmap]
rs41263861	0.82[EUR][1000 genomes]
rs41272749	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs41272777	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55698101	1.00[AFR][1000 genomes]
rs55967487	0.82[EUR][1000 genomes]
rs56196515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56387272	0.84[EUR][1000 genomes]
rs7135926	0.92[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297161	0.90[EUR][1000 genomes]
rs740023	1.00[MEX][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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv525456	chr12:48366449-48376969	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv558789	chr12:48368541-48376869	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12721427	TMEM106C	cis	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48358400-48369800	Weak transcription	Brain Angular Gyrus	brain
2	chr12:48358400-48373000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:48358600-48369400	Weak transcription	Fetal Kidney	kidney
4	chr12:48358600-48381400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:48360200-48369600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:48362400-48370600	Weak transcription	HMEC	breast
8	chr12:48362400-48370800	Weak transcription	NHEK	skin
9	chr12:48363000-48368800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:48363000-48370800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:48363000-48370800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:48363200-48370800	Weak transcription	Fetal Stomach	stomach
13	chr12:48363400-48369000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:48363400-48370800	Weak transcription	Fetal Thymus	thymus
15	chr12:48363400-48374800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr12:48363400-48375000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:48363400-48375000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:48363400-48383000	Weak transcription	Spleen	Spleen
19	chr12:48364000-48370600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:48364400-48369800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:48364400-48371600	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:48364400-48372600	Strong transcription	Fetal Intestine Small	intestine
23	chr12:48364400-48381200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:48364600-48369800	Weak transcription	Placenta	Placenta
25	chr12:48365200-48381600	Weak transcription	Right Atrium	heart
26	chr12:48365400-48381000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:48366000-48370400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:48366200-48370600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:48366200-48381200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:48366200-48381400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:48366200-48381600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:48366600-48368800	Weak transcription	Thymus	Thymus
33	chr12:48366600-48375200	Weak transcription	Gastric	stomach
34	chr12:48366800-48374800	Weak transcription	HepG2	liver
35	chr12:48367800-48369600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr12:48368000-48369200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:48368200-48368600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:48368200-48373800	Weak transcription	Fetal Intestine Large	intestine

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