Variant report

Variant	rs7134878
Chromosome Location	chr12:48417308-48417309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48357498..48359897-chr12:48415530..48417456,2	MCF-7	breast:
2	chr12:48415272..48418773-chr12:48419086..48422802,6	MCF-7	breast:
3	chr12:48212416..48215175-chr12:48415223..48418079,4	MCF-7	breast:
4	chr12:48415871..48417650-chr12:48439843..48442703,2	MCF-7	breast:
5	chr12:48415815..48418237-chr12:48421031..48422834,2	K562	blood:
6	chr12:48406038..48410831-chr12:48411860..48418424,9	MCF-7	breast:
7	chr12:48391315..48400584-chr12:48411914..48418489,16	MCF-7	breast:
8	chr12:48416195..48418689-chr12:48432533..48434686,2	K562	blood:
9	chr12:48367607..48371765-chr12:48415495..48417356,3	MCF-7	breast:
10	chr12:48416900..48419304-chr12:48549157..48552214,3	MCF-7	breast:
11	chr12:48410357..48413530-chr12:48413703..48417962,3	K562	blood:
12	chr12:48416842..48418454-chr12:48435864..48437741,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM106C-1	chr12:48416618-48419252	ENSG00000257985.1

No data

Variant related genes	Relation type
ENSG00000177981	Chromatin interaction
ENSG00000257955	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000139219	Chromatin interaction
ENSG00000134291	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10450783	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168358	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs1635527	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs17122567	0.95[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1793958	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2056448	0.92[EUR][1000 genomes]
rs2408954	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs7134203	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7134878	TMEM106C	cis	parietal	SCAN
rs7134878	DDN	cis	parietal	SCAN
rs7134878	ZNF641	cis	Muscle Skeletal	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48415000-48417800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:48415000-48417800	Enhancers	Fetal Lung	lung
3	chr12:48415000-48417800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr12:48415000-48418000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:48415000-48418200	Enhancers	Fetal Intestine Large	intestine
6	chr12:48415000-48418200	Enhancers	Fetal Intestine Small	intestine
7	chr12:48415200-48418000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:48415200-48418200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48415400-48417800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:48415400-48417800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
11	chr12:48415400-48418000	Enhancers	Fetal Heart	heart
12	chr12:48415400-48418000	Enhancers	HepG2	liver
13	chr12:48415800-48417400	Enhancers	Lung	lung
14	chr12:48415800-48420400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:48416000-48417800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr12:48416000-48418000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:48416200-48417600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
18	chr12:48416400-48417400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
19	chr12:48416400-48417600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:48416400-48417600	Enhancers	Gastric	stomach
21	chr12:48416400-48417800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
22	chr12:48416600-48417800	Enhancers	Duodenum Mucosa	Duodenum
23	chr12:48416800-48417600	Enhancers	Fetal Muscle Trunk	muscle
24	chr12:48416800-48417600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
25	chr12:48416800-48418200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr12:48416800-48423400	Weak transcription	Right Atrium	heart
27	chr12:48417000-48417400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:48417000-48417600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr12:48417000-48417800	Enhancers	Fetal Muscle Leg	muscle
30	chr12:48417000-48418600	Weak transcription	Right Ventricle	heart
31	chr12:48417200-48417400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
32	chr12:48417200-48417400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
33	chr12:48417200-48417400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:48417200-48417400	Enhancers	A549	lung
35	chr12:48417200-48417400	Bivalent Enhancer	K562	blood
36	chr12:48417200-48417600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:48417200-48417600	Enhancers	Pancreas	Pancrea
38	chr12:48417200-48417800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:48417200-48417800	Enhancers	Hela-S3	cervix
40	chr12:48417200-48418000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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