Variant report

Variant	rs6744331
Chromosome Location	chr2:98458002-98458003
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	chr2:98448498..98450073-chr2:98456527..98458387,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10176201	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10194485	1.00[YRI][hapmap]
rs10200949	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10211231	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1071885	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10865055	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11123924	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123949	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123966	0.89[ASN][1000 genomes]
rs11690482	0.89[ASN][1000 genomes]
rs11693874	0.85[ASN][1000 genomes]
rs11888323	0.89[ASN][1000 genomes]
rs11899171	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12712123	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12712174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13003978	0.89[ASN][1000 genomes]
rs13006817	0.89[ASN][1000 genomes]
rs13008503	0.86[ASN][1000 genomes]
rs13010946	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13022778	0.89[ASN][1000 genomes]
rs13034644	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1317178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13405546	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1466020	0.94[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1466924	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1503200	0.89[ASN][1000 genomes]
rs1922280	0.95[ASN][1000 genomes]
rs1922282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2017028	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2091772	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2100058	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141862	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279825	0.83[ASN][1000 genomes]
rs2279826	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2305142	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2309316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2309317	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2309356	0.87[ASN][1000 genomes]
rs3762593	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4274643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4560167	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5865	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs6543108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543109	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6543161	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6543177	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6543202	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6707924	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6709571	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6710813	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6712517	0.83[CEU][hapmap]
rs6719556	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6723466	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6723653	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748809	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6748927	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7558931	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7561104	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562695	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7567397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7574437	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577886	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7586210	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7598116	0.89[ASN][1000 genomes]
rs7602412	0.85[ASN][1000 genomes]
rs7605180	0.89[ASN][1000 genomes]
rs930607	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9308862	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs956696	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9973416	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6744331	TMEM131	Cis_1M	lymphoblastoid	RTeQTL
rs6744331	ANKRD36B	cis	Nerve Tibial	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98405800-98459600	Weak transcription	Stomach Mucosa	stomach
2	chr2:98406400-98469200	Weak transcription	A549	lung
3	chr2:98409400-98484200	Weak transcription	HUVEC	blood vessel
4	chr2:98409800-98485000	Weak transcription	Hela-S3	cervix
5	chr2:98424000-98475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:98424200-98461600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:98425600-98461000	Weak transcription	Brain Germinal Matrix	brain
8	chr2:98428000-98466600	Weak transcription	K562	blood
9	chr2:98428600-98461200	Weak transcription	Fetal Brain Male	brain
10	chr2:98428600-98464600	Weak transcription	HSMMtube	muscle
11	chr2:98428800-98485000	Weak transcription	NHLF	lung
12	chr2:98429000-98470600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:98430000-98467800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:98431000-98466400	Weak transcription	NH-A	brain
15	chr2:98434200-98484000	Weak transcription	NHDF-Ad	bronchial
16	chr2:98434400-98466400	Weak transcription	Brain Substantia Nigra	brain
17	chr2:98434400-98485800	Weak transcription	Lung	lung
18	chr2:98445200-98459800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:98445800-98460000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr2:98446000-98460200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:98446000-98475000	Weak transcription	Gastric	stomach
22	chr2:98447400-98465400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:98447600-98461200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:98447800-98461200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:98447800-98466200	Weak transcription	Psoas Muscle	Psoas
26	chr2:98447800-98479600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:98447800-98502800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:98448000-98461200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:98449000-98458600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:98449600-98482000	Weak transcription	Fetal Kidney	kidney
31	chr2:98450600-98459600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:98450600-98460000	Strong transcription	Primary B cells from cord blood	blood
33	chr2:98451600-98458200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:98451800-98466200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:98452400-98459400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:98453200-98459800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:98454200-98459400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr2:98454400-98460000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:98455000-98458400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:98455400-98458400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:98455400-98458400	Strong transcription	HepG2	liver
42	chr2:98455400-98458600	Strong transcription	Dnd41	blood
43	chr2:98455400-98459400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:98455400-98459400	Strong transcription	GM12878-XiMat	blood
45	chr2:98455400-98459600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:98455400-98459800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr2:98455600-98458400	Strong transcription	Fetal Intestine Large	intestine
48	chr2:98455800-98458400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr2:98456000-98458200	Strong transcription	Ovary	ovary
50	chr2:98456000-98458600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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