Variant report

Variant	rs176901
Chromosome Location	chr14:78078206-78078207
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	chr14:78070489..78072668-chr14:78077080..78079522,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10129280	0.81[CHB][hapmap]
rs10139059	0.81[CHB][hapmap]
rs10139852	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10140195	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10148189	0.90[ASN][1000 genomes]
rs10148244	0.82[ASN][1000 genomes]
rs10162458	0.83[ASN][1000 genomes]
rs10873309	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs11626349	0.88[CHD][hapmap]
rs11626892	0.83[ASN][1000 genomes]
rs12432164	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12587835	0.93[ASN][1000 genomes]
rs13379058	0.95[ASN][1000 genomes]
rs176897	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176898	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs176907	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1990806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2267746	0.81[CHB][hapmap]
rs2267747	0.81[CHB][hapmap]
rs2267748	0.81[CHB][hapmap]
rs2267749	0.81[CHB][hapmap]
rs2267750	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs2299921	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs2299922	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2299924	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs2299927	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2299928	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs2299929	0.99[ASN][1000 genomes]
rs28460392	0.99[ASN][1000 genomes]
rs28472502	0.97[ASN][1000 genomes]
rs4903614	0.81[ASN][1000 genomes]
rs58598324	0.93[ASN][1000 genomes]
rs61990852	0.80[ASN][1000 genomes]
rs7144314	0.84[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap]
rs7157536	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7158771	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8018203	0.82[ASN][1000 genomes]
rs9944097	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[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	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs176901	ALDH6A1	cis	parietal	SCAN
rs176901	TMTC4	trans	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
2	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr14:78063400-78081600	Weak transcription	Fetal Stomach	stomach
4	chr14:78065600-78081400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr14:78066000-78079600	Weak transcription	Dnd41	blood
6	chr14:78066800-78078400	Weak transcription	NHLF	lung
7	chr14:78069200-78081600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr14:78070200-78081600	Weak transcription	Liver	Liver
9	chr14:78070400-78078400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr14:78070400-78079800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr14:78070400-78081400	Weak transcription	Fetal Muscle Leg	muscle
12	chr14:78070600-78078400	Weak transcription	NHDF-Ad	bronchial
13	chr14:78070600-78081400	Weak transcription	Ovary	ovary
14	chr14:78070600-78081600	Weak transcription	Esophagus	oesophagus
15	chr14:78072200-78078400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr14:78072400-78081200	Weak transcription	Fetal Heart	heart
17	chr14:78072400-78081600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr14:78072600-78078400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr14:78072800-78078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr14:78072800-78081400	Weak transcription	Colonic Mucosa	Colon
21	chr14:78073000-78078400	Weak transcription	HepG2	liver
22	chr14:78073400-78078400	Weak transcription	Small Intestine	intestine
23	chr14:78073400-78081600	Weak transcription	Psoas Muscle	Psoas
24	chr14:78074200-78078600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr14:78074200-78081400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr14:78074400-78078400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr14:78074600-78078400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr14:78074600-78078400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr14:78074600-78079400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr14:78074600-78079600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr14:78074600-78081200	Weak transcription	Fetal Intestine Large	intestine
32	chr14:78074600-78081400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:78074600-78081400	Weak transcription	Right Atrium	heart
34	chr14:78074600-78081600	Weak transcription	Fetal Thymus	thymus
35	chr14:78074800-78078400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr14:78074800-78078600	Weak transcription	Brain Anterior Caudate	brain
37	chr14:78074800-78081400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr14:78075000-78078400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr14:78075000-78078400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr14:78075000-78078600	Weak transcription	Brain Angular Gyrus	brain
41	chr14:78075000-78078600	Weak transcription	Fetal Kidney	kidney
42	chr14:78075000-78079600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr14:78075000-78079600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr14:78075200-78078400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr14:78075200-78078400	Weak transcription	Adipose Nuclei	Adipose
46	chr14:78075200-78078400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr14:78075200-78079400	Weak transcription	Primary T cells from cord blood	blood
48	chr14:78075200-78079800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr14:78075200-78080400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr14:78075600-78078400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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