Variant report

Variant	rs2305142
Chromosome Location	chr2:98375722-98375723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:98373619..98375783-chr2:98377348..98379631,2	MCF-7	breast:
2	chr2:98279652..98281839-chr2:98374236..98375884,2	MCF-7	breast:
3	chr2:98371016..98372901-chr2:98373770..98376457,3	K562	blood:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction
ENSG00000201806	Chromatin interaction
ENSG00000228486	Chromatin interaction
ENSG00000115073	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10168543	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10169155	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10180434	0.85[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs10180837	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10182941	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs10184393	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10188497	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10188713	0.85[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10189414	0.81[EUR][1000 genomes]
rs10192322	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10206684	0.81[EUR][1000 genomes]
rs10208070	0.83[EUR][1000 genomes]
rs11893437	0.84[CEU][hapmap]
rs11894541	0.80[EUR][1000 genomes]
rs11897301	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12712117	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12712147	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12712162	0.81[EUR][1000 genomes]
rs12712163	0.80[EUR][1000 genomes]
rs12712174	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs12991122	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13000585	0.81[EUR][1000 genomes]
rs13008678	0.82[EUR][1000 genomes]
rs13012645	0.84[EUR][1000 genomes]
rs1317178	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs13427422	0.81[EUR][1000 genomes]
rs1446327	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1466020	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1922282	0.81[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs1960329	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1982336	0.96[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2293679	0.85[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2309316	0.81[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs34305873	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35185431	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35203092	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35402416	0.84[EUR][1000 genomes]
rs35807655	0.81[EUR][1000 genomes]
rs3821053	0.85[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4274643	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs5865	0.81[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6543108	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs6543210	0.81[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs6707719	0.85[CEU][hapmap]
rs6707750	0.83[EUR][1000 genomes]
rs6709571	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs6710813	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs6712078	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6721323	0.96[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6736735	0.92[CEU][hapmap];0.80[MEX][hapmap];0.80[EUR][1000 genomes]
rs6748809	0.88[JPT][hapmap]
rs6748927	0.88[JPT][hapmap]
rs6751727	0.81[EUR][1000 genomes]
rs718159	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7567397	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs7591374	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7594928	0.81[EUR][1000 genomes]
rs7595039	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9808558	0.85[CEU][hapmap];0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2305142	TEKT4	cis	cerebellum	SCAN
rs2305142	INPP4A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98352200-98398800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:98359200-98382400	Weak transcription	Psoas Muscle	Psoas
3	chr2:98365400-98375800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:98366200-98400000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:98366400-98376800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr2:98366400-98384600	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr2:98366800-98377600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:98367200-98385000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:98367400-98380000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:98368000-98393800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:98368400-98377000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:98368400-98383600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:98368600-98413000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:98369200-98381200	Weak transcription	Fetal Heart	heart
15	chr2:98369400-98376600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:98369600-98398800	Strong transcription	Fetal Muscle Leg	muscle
17	chr2:98369800-98384800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:98370200-98376800	Weak transcription	NHDF-Ad	bronchial
19	chr2:98370200-98392600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:98370400-98376600	Strong transcription	Primary T cells from cord blood	blood
21	chr2:98370400-98382800	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:98370400-98383600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:98370400-98386400	Strong transcription	Fetal Intestine Small	intestine
24	chr2:98370600-98381800	Strong transcription	Lung	lung
25	chr2:98370600-98384400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr2:98370600-98384400	Strong transcription	Placenta	Placenta
27	chr2:98370600-98392400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:98370600-98393800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:98370600-98407600	Weak transcription	HUVEC	blood vessel
30	chr2:98370800-98384200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:98370800-98384400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:98370800-98384400	Strong transcription	Fetal Stomach	stomach
33	chr2:98371000-98375800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:98371000-98376600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr2:98371000-98377800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:98371000-98379200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:98371000-98379800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:98371000-98379800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:98371000-98383000	Strong transcription	Brain Angular Gyrus	brain
40	chr2:98371000-98383000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:98371000-98383400	Strong transcription	Brain Cingulate Gyrus	brain
42	chr2:98371000-98384800	Strong transcription	Fetal Intestine Large	intestine
43	chr2:98371200-98377400	Strong transcription	Spleen	Spleen
44	chr2:98371200-98383000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:98371200-98383000	Strong transcription	Brain Anterior Caudate	brain
46	chr2:98371200-98383000	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr2:98371200-98383200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:98371200-98383400	Strong transcription	Colonic Mucosa	Colon
49	chr2:98371200-98384400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:98371200-98384400	Strong transcription	Stomach Smooth Muscle	stomach

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