Variant report

Variant	rs3213945
Chromosome Location	chr2:178402786-178402787
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178400127..178404094-chr2:178416141..178417810,3	MCF-7	breast:
2	chr2:178401949..178404260-chr2:178404405..178406042,2	K562	blood:
3	chr2:178381975..178383785-chr2:178400667..178403415,2	K562	blood:
4	chr2:178379160..178381107-chr2:178401992..178404272,2	K562	blood:

Variant related genes	Relation type
ENSG00000196659	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10170546	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10170667	0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs10194648	0.82[ASN][1000 genomes]
rs10196345	0.85[EUR][1000 genomes]
rs10201153	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10497500	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs10497501	0.82[JPT][hapmap]
rs10497502	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs10497503	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10497508	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.89[ASN][1000 genomes]
rs10930792	0.81[ASN][1000 genomes]
rs12469386	0.85[JPT][hapmap]
rs12612857	0.86[JPT][hapmap]
rs12615367	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12616093	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12618139	1.00[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap];0.93[ASN][1000 genomes]
rs12990729	0.81[ASN][1000 genomes]
rs13000048	0.85[JPT][hapmap]
rs13004955	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13404970	0.84[EUR][1000 genomes]
rs13430517	0.85[EUR][1000 genomes]
rs1348848	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1348849	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1348850	0.95[JPT][hapmap]
rs1374437	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1405713	0.86[JPT][hapmap]
rs1453370	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1548067	0.86[JPT][hapmap]
rs16865203	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs16865216	0.89[ASN][1000 genomes]
rs16865229	0.89[ASN][1000 genomes]
rs16865291	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs16865328	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16865331	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16865433	0.82[EUR][1000 genomes]
rs1901825	0.84[JPT][hapmap]
rs1901826	0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs1979058	0.81[ASN][1000 genomes]
rs2034678	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2060929	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2084233	0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2121430	0.85[JPT][hapmap]
rs2166558	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2197611	0.82[ASN][1000 genomes]
rs2364853	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2364854	0.85[JPT][hapmap]
rs3769995	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs3769996	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.93[ASN][1000 genomes]
rs3769997	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs3770002	0.86[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs3813259	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3902850	0.81[ASN][1000 genomes]
rs4243388	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4528793	0.86[JPT][hapmap]
rs4893821	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4893822	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4893823	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs4893825	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4893935	0.85[JPT][hapmap]
rs4893936	0.84[JPT][hapmap]
rs4893950	0.84[JPT][hapmap]
rs4893951	0.88[ASN][1000 genomes]
rs4893957	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs4893959	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4893961	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4893962	0.95[JPT][hapmap]
rs4893965	0.86[JPT][hapmap]
rs56942680	0.85[ASN][1000 genomes]
rs57273542	0.89[ASN][1000 genomes]
rs57295810	0.93[ASN][1000 genomes]
rs57527255	0.92[ASN][1000 genomes]
rs57541536	0.92[ASN][1000 genomes]
rs57562172	0.85[EUR][1000 genomes]
rs57733896	0.92[ASN][1000 genomes]
rs57948641	0.92[ASN][1000 genomes]
rs58297927	0.92[ASN][1000 genomes]
rs58483300	0.85[ASN][1000 genomes]
rs59111239	0.89[ASN][1000 genomes]
rs59421055	0.95[ASN][1000 genomes]
rs59504156	0.90[ASN][1000 genomes]
rs59666005	0.85[EUR][1000 genomes]
rs60642012	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60670838	0.89[ASN][1000 genomes]
rs60733259	0.85[ASN][1000 genomes]
rs6433670	0.82[ASN][1000 genomes]
rs6433673	0.83[ASN][1000 genomes]
rs6710575	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6742951	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7587604	0.85[JPT][hapmap]
rs7591807	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7604673	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7606235	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7607450	0.82[ASN][1000 genomes]
rs8941	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9288004	0.85[EUR][1000 genomes]
rs9288005	0.85[EUR][1000 genomes]
rs952746	0.85[JPT][hapmap]
rs9679607	0.81[ASN][1000 genomes]
rs9789582	0.81[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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3213945	TTC30A	cis	lymphoblastoid	seeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178335000-178410600	Weak transcription	Thymus	Thymus
2	chr2:178338000-178403000	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:178349800-178407800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:178350000-178407000	Weak transcription	Osteobl	bone
5	chr2:178356000-178405400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:178358600-178406000	Weak transcription	Ovary	ovary
7	chr2:178358600-178417000	Weak transcription	Aorta	Aorta
8	chr2:178360600-178405400	Weak transcription	NH-A	brain
9	chr2:178364400-178416600	Weak transcription	Esophagus	oesophagus
10	chr2:178372600-178405400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:178372800-178416600	Weak transcription	A549	lung
12	chr2:178375600-178413800	Weak transcription	K562	blood
13	chr2:178376200-178407800	Weak transcription	Left Ventricle	heart
14	chr2:178376200-178416600	Weak transcription	Pancreas	Pancrea
15	chr2:178376600-178407600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:178378400-178410000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:178379600-178407600	Weak transcription	Fetal Kidney	kidney
18	chr2:178379800-178406000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:178385400-178405000	Weak transcription	GM12878-XiMat	blood
20	chr2:178386000-178407400	Weak transcription	HSMMtube	muscle
21	chr2:178386800-178405400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr2:178388600-178416600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:178388800-178405400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:178389000-178405200	Weak transcription	Fetal Intestine Large	intestine
25	chr2:178389000-178407800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:178389000-178408200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:178389000-178416800	Weak transcription	Small Intestine	intestine
28	chr2:178389200-178406000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:178389200-178416600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:178389600-178403200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:178389800-178402800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:178389800-178406800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr2:178389800-178407600	Weak transcription	Adipose Nuclei	Adipose
34	chr2:178389800-178410200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:178389800-178416800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:178390600-178402800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:178390600-178416600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:178390800-178403200	Weak transcription	Liver	Liver
39	chr2:178390800-178407400	Weak transcription	Fetal Stomach	stomach
40	chr2:178391000-178413400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:178391200-178406000	Weak transcription	Fetal Thymus	thymus
42	chr2:178391400-178407200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:178391800-178408000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:178392000-178416800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:178393200-178403000	Weak transcription	HSMM	muscle
46	chr2:178393400-178402800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:178397600-178410600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:178399800-178404000	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:178400200-178403800	Strong transcription	HepG2	liver
50	chr2:178400400-178403000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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