Variant report

Variant	rs6960004
Chromosome Location	chr7:127734012-127734013
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	chr7:127724656..127727376-chr7:127732836..127734989,2	MCF-7	breast:
2	chr7:127724628..127729204-chr7:127729479..127734634,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs178733	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs184430	0.86[ASN][1000 genomes]
rs322738	0.82[ASN][1000 genomes]
rs322756	0.82[ASN][1000 genomes]
rs322760	0.83[ASN][1000 genomes]
rs322761	0.83[ASN][1000 genomes]
rs322762	0.83[ASN][1000 genomes]
rs322765	0.83[ASN][1000 genomes]
rs322766	0.83[ASN][1000 genomes]
rs322768	0.84[ASN][1000 genomes]
rs322770	0.84[ASN][1000 genomes]
rs322771	0.86[ASN][1000 genomes]
rs322775	0.86[ASN][1000 genomes]
rs322778	0.86[ASN][1000 genomes]
rs322780	0.91[ASN][1000 genomes]
rs322782	0.91[ASN][1000 genomes]
rs322783	0.92[ASN][1000 genomes]
rs322784	0.92[ASN][1000 genomes]
rs322785	0.92[ASN][1000 genomes]
rs322786	0.94[ASN][1000 genomes]
rs322787	0.95[ASN][1000 genomes]
rs322790	0.95[ASN][1000 genomes]
rs322791	0.95[ASN][1000 genomes]
rs322806	0.95[ASN][1000 genomes]
rs322807	0.94[CHB][hapmap];0.95[ASN][1000 genomes]
rs322808	0.95[ASN][1000 genomes]
rs322809	0.95[ASN][1000 genomes]
rs322811	0.97[ASN][1000 genomes]
rs322812	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs322818	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757764	0.88[ASW][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap]
rs5028619	0.95[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	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6960004	TMEM229A	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127707800-127742200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:127710600-127737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:127711600-127735600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr7:127711600-127736400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr7:127711800-127737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:127712200-127738200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr7:127713000-127735000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr7:127713000-127737200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:127713200-127736400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:127713400-127736400	Strong transcription	NHEK	skin
11	chr7:127713800-127738800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr7:127714400-127735000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr7:127714400-127738000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr7:127714800-127734400	Strong transcription	Dnd41	blood
15	chr7:127715800-127738400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:127717000-127738000	Weak transcription	Fetal Kidney	kidney
17	chr7:127717200-127736600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr7:127717200-127738600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:127717600-127736600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:127717600-127738800	Strong transcription	Liver	Liver
21	chr7:127717800-127736600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:127718200-127736400	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr7:127718200-127736400	Strong transcription	Stomach Smooth Muscle	stomach
24	chr7:127718400-127736600	Strong transcription	Gastric	stomach
25	chr7:127719200-127736400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr7:127720000-127736000	Weak transcription	Psoas Muscle	Psoas
27	chr7:127720600-127738200	Strong transcription	GM12878-XiMat	blood
28	chr7:127721200-127735800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:127721400-127734800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:127721400-127735000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr7:127722400-127738400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:127723600-127736800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:127723800-127735000	Strong transcription	Aorta	Aorta
34	chr7:127723800-127735800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr7:127724000-127735600	Strong transcription	Placenta	Placenta
36	chr7:127724000-127739800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:127724200-127737000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:127724400-127735800	Strong transcription	Primary T cells from cord blood	blood
39	chr7:127724600-127737600	Strong transcription	Thymus	Thymus
40	chr7:127724600-127743600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr7:127724800-127734400	Strong transcription	Fetal Thymus	thymus
42	chr7:127724800-127734800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr7:127724800-127735000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr7:127724800-127736600	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr7:127725200-127737800	Strong transcription	Fetal Muscle Leg	muscle
46	chr7:127725400-127734600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr7:127725600-127736800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr7:127725800-127734600	Weak transcription	Right Atrium	heart
49	chr7:127725800-127739000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr7:127726000-127737800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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