Variant report

Variant	rs10130181
Chromosome Location	chr14:39821153-39821154
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39803770..39806205-chr14:39819657..39822349,3	MCF-7	breast:
2	chr14:39820058..39821660-chr17:57919324..57920966,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10047876	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs10132190	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10133746	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs10134065	0.93[ASN][1000 genomes]
rs10136490	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs10140997	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.83[AMR][1000 genomes]
rs10142029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10144377	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145757	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10146622	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10147286	1.00[CHB][hapmap]
rs10220689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10483538	0.82[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12185014	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12433987	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437261	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17109168	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[ASN][1000 genomes]
rs17622868	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17693279	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1955716	0.85[CHB][hapmap]
rs1998885	0.85[CHB][hapmap]
rs1998886	0.85[CHB][hapmap]
rs2103795	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2179973	0.85[ASN][1000 genomes]
rs2415541	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs28398804	0.85[ASN][1000 genomes]
rs28419351	0.85[ASN][1000 genomes]
rs28454173	0.85[ASN][1000 genomes]
rs28568594	0.85[ASN][1000 genomes]
rs28571663	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28630597	1.00[AFR][1000 genomes]
rs28704775	0.85[ASN][1000 genomes]
rs28756493	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28823387	0.83[AMR][1000 genomes]
rs28871954	0.85[ASN][1000 genomes]
rs2899887	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783291	0.82[CHB][hapmap]
rs4316662	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902458	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4902559	1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61999073	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs61999077	0.85[ASN][1000 genomes]
rs61999079	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62000686	0.96[AMR][1000 genomes]
rs62000696	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62000708	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62000709	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62000710	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62000711	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62000715	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62000720	0.86[ASN][1000 genomes]
rs62001106	0.85[ASN][1000 genomes]
rs7146753	0.85[ASN][1000 genomes]
rs7155173	1.00[YRI][hapmap]
rs7156962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[ASN][1000 genomes]
rs7158282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8006076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.95[ASN][1000 genomes]
rs8007036	0.95[ASN][1000 genomes]
rs9322999	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[ASN][1000 genomes]
rs9805937	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[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	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10130181	TRAPPC6B	cis	multi-tissue	Pritchard
rs10130181	MBIP	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39756200-39828400	Weak transcription	Brain Germinal Matrix	brain
2	chr14:39757400-39843800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr14:39767200-39833800	Weak transcription	Small Intestine	intestine
4	chr14:39770800-39872400	Weak transcription	Colonic Mucosa	Colon
5	chr14:39786600-39828600	Weak transcription	Spleen	Spleen
6	chr14:39786800-39823000	Strong transcription	Liver	Liver
7	chr14:39792800-39841600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr14:39793000-39822200	Weak transcription	Fetal Lung	lung
9	chr14:39794400-39843200	Weak transcription	HUVEC	blood vessel
10	chr14:39796400-39828400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr14:39797000-39837400	Weak transcription	Brain Substantia Nigra	brain
12	chr14:39802000-39835600	Weak transcription	Esophagus	oesophagus
13	chr14:39802000-39841200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr14:39802600-39835400	Weak transcription	Psoas Muscle	Psoas
15	chr14:39802800-39822000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr14:39802800-39828400	Weak transcription	Ovary	ovary
17	chr14:39802800-39828400	Weak transcription	Pancreas	Pancrea
18	chr14:39802800-39828600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr14:39802800-39835400	Weak transcription	Gastric	stomach
20	chr14:39802800-39839400	Weak transcription	Aorta	Aorta
21	chr14:39803000-39835400	Weak transcription	Right Ventricle	heart
22	chr14:39803000-39845800	Weak transcription	NHEK	skin
23	chr14:39803200-39824600	Weak transcription	Brain Hippocampus Middle	brain
24	chr14:39803200-39833000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr14:39803200-39838400	Weak transcription	Thymus	Thymus
26	chr14:39803200-39843400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:39803200-39845800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr14:39803400-39843800	Weak transcription	HMEC	breast
29	chr14:39807000-39824400	Weak transcription	NH-A	brain
30	chr14:39807400-39836000	Weak transcription	Brain Anterior Caudate	brain
31	chr14:39808400-39828400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr14:39808400-39828800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr14:39808400-39841200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr14:39808600-39828400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr14:39808600-39828800	Weak transcription	Fetal Heart	heart
36	chr14:39808800-39822200	Weak transcription	A549	lung
37	chr14:39809600-39822400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr14:39809600-39832800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr14:39809800-39828800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr14:39810000-39835200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr14:39811800-39823200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr14:39812200-39845800	Weak transcription	Stomach Mucosa	stomach
43	chr14:39812400-39832800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr14:39812400-39833600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr14:39812600-39823200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr14:39813800-39822800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr14:39813800-39823000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr14:39814400-39823400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr14:39814600-39823200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr14:39815600-39832800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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