Variant report

Variant	rs1541408
Chromosome Location	chr12:48348352-48348353
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48341895..48344737-chr12:48347947..48350941,3	K562	blood:
2	chr12:48290096..48306593-chr12:48332606..48350271,44	MCF-7	breast:
3	chr12:48343273..48345305-chr12:48347041..48349607,2	MCF-7	breast:
4	chr12:48347971..48349706-chr12:48354609..48357059,2	MCF-7	breast:
5	chr12:48337421..48339727-chr12:48348343..48351115,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111424	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11168244	1.00[LWK][hapmap]
rs11168331	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11503871	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11503873	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12300271	1.00[GIH][hapmap]
rs12313208	1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12721425	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12721426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12721427	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	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs2408878	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35000511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077869	1.00[CHB][hapmap]
rs41272749	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs41272777	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55698101	1.00[AFR][1000 genomes]
rs56196515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135926	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297161	0.82[EUR][1000 genomes]
rs740023	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1541408	TMEM106C	cis	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48338400-48348800	Enhancers	HMEC	breast
2	chr12:48344400-48349000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:48345200-48348800	Enhancers	NHEK	skin
4	chr12:48345800-48348400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:48346600-48348600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:48346800-48349200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr12:48347000-48349400	Enhancers	Placenta	Placenta
8	chr12:48347200-48349000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr12:48347200-48349200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:48347200-48349200	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr12:48347400-48348400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:48347400-48349000	Enhancers	Colonic Mucosa	Colon
13	chr12:48347600-48349200	Enhancers	Fetal Intestine Large	intestine
14	chr12:48347600-48349200	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr12:48347600-48349600	Enhancers	Fetal Lung	lung
16	chr12:48347800-48348800	Enhancers	Fetal Intestine Small	intestine
17	chr12:48348000-48348600	Enhancers	Fetal Thymus	thymus
18	chr12:48348000-48349200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr12:48348200-48348600	Enhancers	Dnd41	blood
20	chr12:48348200-48351400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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