Variant report

Variant	rs4953442
Chromosome Location	chr2:47245022-47245023
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47219377..47221556-chr2:47242383..47245078,2	MCF-7	breast:
2	chr2:47243930..47246637-chr2:47261701..47264377,2	MCF-7	breast:
3	chr2:47242011..47245119-chr2:47248786..47251159,3	K562	blood:
4	chr2:47244477..47246233-chr2:47418737..47420783,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10172245	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196023	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1036291	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1036292	0.93[CHB][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap]
rs1036293	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs11896335	0.93[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs12466088	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12469879	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12615391	0.93[CHB][hapmap]
rs13015901	0.86[CHB][hapmap]
rs1865258	0.87[CHD][hapmap]
rs2163982	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs4324364	0.90[ASN][1000 genomes]
rs4952859	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4952860	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4953440	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4953441	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs4953443	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6739975	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7558419	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs7607573	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv518312	chr2:47224927-47262137	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv984532	chr2:47237908-47270533	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv581751	chr2:47243124-47255723	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4953442	TTC7A	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47213600-47256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:47214000-47262000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:47215600-47245200	Strong transcription	Primary B cells from peripheral blood	blood
4	chr2:47222000-47260600	Weak transcription	Small Intestine	intestine
5	chr2:47223600-47246800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:47229200-47248600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr2:47230200-47302800	Strong transcription	Dnd41	blood
8	chr2:47232000-47265000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:47232400-47257000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:47234400-47283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:47236000-47278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:47236600-47253600	Strong transcription	Fetal Intestine Small	intestine
13	chr2:47236600-47259200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:47236600-47259200	Weak transcription	Fetal Kidney	kidney
15	chr2:47236800-47251600	Weak transcription	Fetal Lung	lung
16	chr2:47237000-47246800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:47237000-47247400	Strong transcription	Fetal Stomach	stomach
18	chr2:47237000-47254200	Weak transcription	Ovary	ovary
19	chr2:47237000-47260400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:47237200-47249200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:47237400-47245200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:47238000-47247400	Strong transcription	Primary T cells from cord blood	blood
23	chr2:47238200-47253400	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr2:47238200-47253600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr2:47238200-47253800	Strong transcription	HepG2	liver
26	chr2:47239400-47249200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:47239800-47246000	Weak transcription	Fetal Heart	heart
28	chr2:47240000-47249800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:47240200-47251800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:47240200-47256000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:47240600-47248800	Weak transcription	Liver	Liver
32	chr2:47240600-47249200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:47240800-47251400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:47241400-47250400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:47242000-47249000	Weak transcription	Colonic Mucosa	Colon
36	chr2:47242000-47249200	Weak transcription	Brain Germinal Matrix	brain
37	chr2:47242200-47247000	Weak transcription	Fetal Intestine Large	intestine
38	chr2:47242200-47247000	Weak transcription	Right Ventricle	heart
39	chr2:47242200-47247800	Weak transcription	Gastric	stomach
40	chr2:47242200-47250400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:47242200-47253400	Weak transcription	HMEC	breast
42	chr2:47242400-47245400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:47242600-47246400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:47242800-47246600	Strong transcription	Thymus	Thymus
45	chr2:47243000-47246000	Weak transcription	Fetal Brain Male	brain
46	chr2:47243000-47247000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:47243200-47247400	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:47243400-47246800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:47243400-47247400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:47243600-47246600	Weak transcription	Fetal Brain Female	brain

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