Variant report

Variant	rs7954234
Chromosome Location	chr12:22217864-22217865
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	chr12:22215672..22218062-chr12:22219622..22221151,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12423101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423142	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12424838	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12427354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12578369	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs12816385	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12818845	0.97[ASN][1000 genomes]
rs12827678	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2193379	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418036	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487271	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6487278	0.96[ASN][1000 genomes]
rs67339960	0.92[ASN][1000 genomes]
rs71448623	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7300481	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969132	0.93[ASN][1000 genomes]
rs7978726	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[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	nsv1051073	chr12:21910875-22271209	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2758298	chr12:22140834-22339299	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2759883	chr12:22140834-22736907	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised 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
4	nsv438196	chr12:22195202-22234058	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv1850259	chr12:22198865-22244741	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7954234	TTTY6	N/A	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:22200000-22218200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:22200000-22220200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:22200000-22220200	Weak transcription	Lung	lung
4	chr12:22200200-22219600	Weak transcription	Aorta	Aorta
5	chr12:22200400-22220400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:22200800-22220800	Weak transcription	Fetal Heart	heart
7	chr12:22201400-22220400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:22201800-22219000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:22202000-22218000	Weak transcription	Psoas Muscle	Psoas
10	chr12:22202000-22219600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:22202000-22220200	Weak transcription	Fetal Brain Male	brain
12	chr12:22202200-22218000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:22202200-22223800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:22203800-22220200	Weak transcription	Esophagus	oesophagus
15	chr12:22203800-22220200	Weak transcription	Small Intestine	intestine
16	chr12:22203800-22235200	Weak transcription	Gastric	stomach
17	chr12:22204600-22219400	Weak transcription	Stomach Mucosa	stomach
18	chr12:22204600-22223400	Weak transcription	Pancreas	Pancrea
19	chr12:22205200-22222200	Weak transcription	Fetal Intestine Small	intestine
20	chr12:22207000-22218400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:22207000-22220200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:22207600-22218800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:22207600-22219400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:22207800-22219000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:22208000-22219600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr12:22208000-22219800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:22208000-22219800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:22208400-22219600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr12:22208400-22219800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:22208400-22220800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:22208600-22219800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:22208800-22220400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr12:22209800-22222000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:22209800-22223200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:22209800-22229200	Weak transcription	Thymus	Thymus
36	chr12:22210000-22219400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:22210000-22219800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr12:22210000-22221200	Strong transcription	Liver	Liver
39	chr12:22210200-22218600	Weak transcription	Left Ventricle	heart
40	chr12:22210200-22219200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr12:22210200-22220200	Weak transcription	Spleen	Spleen
42	chr12:22210400-22221200	Weak transcription	Right Ventricle	heart
43	chr12:22211200-22218000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr12:22211200-22219600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:22211400-22219600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:22211600-22218800	Strong transcription	HSMM	muscle
47	chr12:22211600-22221000	Weak transcription	Fetal Stomach	stomach
48	chr12:22212000-22218000	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:22212000-22218400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr12:22212000-22220600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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