Variant report

Variant	rs11172304
Chromosome Location	chr12:58097862-58097863
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	chr12:58096280..58099117-chr12:58103405..58105701,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10082911	0.90[AFR][1000 genomes]
rs1050045	0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.83[MKK][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10783844	0.90[AFR][1000 genomes]
rs10877007	0.87[AFR][1000 genomes]
rs12368653	0.80[TSI][hapmap]
rs1633360	0.85[AFR][1000 genomes]
rs238517	0.83[AMR][1000 genomes]
rs3825078	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs7138608	0.82[ASN][1000 genomes]
rs7295422	0.83[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7311632	0.83[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7952989	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7979246	0.88[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs799265	0.83[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.85[MKK][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs799267	0.81[AMR][1000 genomes];0.82[ASN][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	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv508676	chr12:58045136-58098538	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
4	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	esv1820402	chr12:58092554-58110211	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11172304	TSFM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58088800-58099400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:58088800-58099400	Weak transcription	Small Intestine	intestine
3	chr12:58089000-58109400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:58089000-58110000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:58089200-58103400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:58089200-58115400	Weak transcription	Fetal Heart	heart
7	chr12:58089600-58098600	Weak transcription	Hela-S3	cervix
8	chr12:58089800-58101200	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:58090200-58098800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:58091000-58109800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:58091000-58110200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:58091200-58101200	Weak transcription	Colonic Mucosa	Colon
13	chr12:58091200-58109600	Weak transcription	Right Ventricle	heart
14	chr12:58091200-58116600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:58091400-58108600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:58091400-58110200	Weak transcription	HUVEC	blood vessel
17	chr12:58091400-58111600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:58092200-58106600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:58092600-58099400	Weak transcription	Lung	lung
20	chr12:58092600-58103800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:58092600-58106400	Weak transcription	Aorta	Aorta
22	chr12:58092600-58106600	Weak transcription	Esophagus	oesophagus
23	chr12:58092600-58107600	Weak transcription	Pancreas	Pancrea
24	chr12:58092800-58109000	Weak transcription	HSMMtube	muscle
25	chr12:58092800-58109200	Weak transcription	HepG2	liver
26	chr12:58092800-58109400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:58093000-58106600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:58093400-58106400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr12:58093400-58109600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:58093400-58115400	Weak transcription	Fetal Brain Male	brain
31	chr12:58093600-58109000	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:58094400-58106400	Weak transcription	Spleen	Spleen
33	chr12:58094400-58119600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:58094600-58099600	Weak transcription	Left Ventricle	heart
35	chr12:58094600-58101000	Weak transcription	Gastric	stomach
36	chr12:58095400-58098200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:58095400-58100000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:58095400-58101400	Strong transcription	Fetal Lung	lung
39	chr12:58095400-58103000	Strong transcription	Liver	Liver
40	chr12:58095600-58102400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:58095800-58098000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:58095800-58098000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:58095800-58098000	Strong transcription	Fetal Thymus	thymus
44	chr12:58095800-58101600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:58096000-58098400	Strong transcription	Fetal Brain Female	brain
46	chr12:58096000-58099400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:58096000-58100600	Strong transcription	Placenta	Placenta
48	chr12:58096000-58101600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:58096000-58102200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr12:58096200-58098000	Strong transcription	Brain Hippocampus Middle	brain

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