Variant report

Variant	rs4244848
Chromosome Location	chr12:29925273-29925274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29920312..29922564-chr12:29924302..29925807,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10743672	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743673	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743674	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771578	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10771579	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771580	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10843501	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10843502	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10843503	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843504	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609828	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12231167	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12810794	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1551930	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2882467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302335	0.92[AMR][1000 genomes]
rs302336	0.92[AMR][1000 genomes]
rs302337	0.92[AMR][1000 genomes]
rs302338	0.92[AMR][1000 genomes]
rs4244849	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931215	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931216	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4931217	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931218	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4931219	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56703053	0.81[AMR][1000 genomes]
rs67168837	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7967779	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv898953	chr12:29905322-29989292	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4244848	TMTC1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29904200-29928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:29904600-29927800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:29906600-29928400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:29916000-29931400	Weak transcription	Pancreas	Pancrea
5	chr12:29916800-29925400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:29917000-29926000	Weak transcription	Right Ventricle	heart
7	chr12:29919800-29926000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:29919800-29927600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:29920400-29928400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr12:29921200-29926600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:29921400-29927400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:29921600-29934000	Weak transcription	Fetal Kidney	kidney
13	chr12:29922600-29926000	Weak transcription	Ovary	ovary
14	chr12:29922600-29926400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:29922600-29926400	Weak transcription	Spleen	Spleen
16	chr12:29922600-29929600	Weak transcription	HSMM	muscle
17	chr12:29922600-29931000	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:29922600-29931800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:29922600-29934000	Weak transcription	NHLF	lung
20	chr12:29922800-29926000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:29922800-29926000	Weak transcription	Left Ventricle	heart
22	chr12:29922800-29926000	Weak transcription	Psoas Muscle	Psoas
23	chr12:29922800-29926000	Weak transcription	Right Atrium	heart
24	chr12:29922800-29926000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:29922800-29928200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:29922800-29928200	Weak transcription	Fetal Muscle Leg	muscle
27	chr12:29922800-29930600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:29922800-29931200	Weak transcription	Aorta	Aorta
29	chr12:29922800-29933800	Weak transcription	Hela-S3	cervix
30	chr12:29923400-29925800	Weak transcription	Fetal Heart	heart
31	chr12:29924000-29925600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:29924000-29926400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:29924000-29926800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:29924200-29925600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr12:29924200-29925600	Enhancers	NHDF-Ad	bronchial
36	chr12:29924200-29927800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:29924400-29925400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:29924400-29925400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr12:29924400-29925400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:29924400-29925400	Enhancers	NHEK	skin
41	chr12:29924400-29927000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr12:29924600-29925400	Enhancers	Osteobl	bone
43	chr12:29924600-29925600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr12:29924600-29925600	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr12:29924600-29925600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr12:29924600-29931600	Weak transcription	Adipose Nuclei	Adipose
47	chr12:29924800-29925400	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr12:29924800-29925600	Flanking Active TSS	HMEC	breast
49	chr12:29925000-29925600	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr12:29925200-29928400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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