Variant report

Variant	rs2060929
Chromosome Location	chr2:178280031-178280032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178277628..178281147-chr2:178283035..178284877,3	K562	blood:
2	chr2:178128805..178133171-chr2:178278601..178282865,4	K562	blood:
3	chr2:178271907..178274801-chr2:178278003..178280488,3	K562	blood:
4	chr2:178129794..178132152-chr2:178278601..178281351,2	K562	blood:
5	chr2:178258938..178262041-chr2:178277248..178280629,3	K562	blood:

Variant related genes	Relation type
ENSG00000116044	Chromatin interaction
ENSG00000222043	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10165785	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10170546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10170667	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10176632	0.81[ASN][1000 genomes]
rs10194648	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10201153	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10208150	0.82[ASN][1000 genomes]
rs10497501	0.89[CEU][hapmap]
rs10497502	0.85[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10497503	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10497508	0.91[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10803909	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10930792	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11688684	0.85[JPT][hapmap]
rs11893448	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12104588	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12469386	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12474344	0.80[JPT][hapmap]
rs12612857	0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap]
rs12615367	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs12616093	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs12616443	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12618139	0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12693120	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990594	0.85[JPT][hapmap]
rs12990729	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12996447	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13000048	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13004955	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13022567	0.80[JPT][hapmap]
rs13027959	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1348848	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1348849	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1348850	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs1374437	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1405713	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs1453370	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1453371	0.81[ASN][1000 genomes]
rs1453373	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1548067	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs16865203	0.91[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs16865216	0.89[ASN][1000 genomes]
rs16865229	0.89[ASN][1000 genomes]
rs16865291	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs16865328	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs16865331	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1901824	0.88[ASN][1000 genomes]
rs1901825	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1901826	0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1901829	0.90[ASN][1000 genomes]
rs1979058	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2034678	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2084233	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2121430	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2166558	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2197611	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2364845	0.88[ASN][1000 genomes]
rs2364853	0.83[ASN][1000 genomes]
rs2364854	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3213945	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3769995	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3769996	0.90[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3769997	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3770002	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3813259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3902850	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4243388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341974	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4528793	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs4893821	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4893822	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4893823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4893824	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4893825	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4893931	0.84[ASN][1000 genomes]
rs4893932	0.88[ASN][1000 genomes]
rs4893934	0.88[ASN][1000 genomes]
rs4893935	0.81[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4893936	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4893938	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4893941	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893944	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4893945	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4893946	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4893950	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4893951	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4893954	0.91[ASN][1000 genomes]
rs4893957	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4893959	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893961	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4893962	0.89[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4893965	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs56942680	0.84[ASN][1000 genomes]
rs57273542	0.88[ASN][1000 genomes]
rs57295810	0.85[ASN][1000 genomes]
rs57527255	0.86[ASN][1000 genomes]
rs57541536	0.86[ASN][1000 genomes]
rs57733896	0.84[ASN][1000 genomes]
rs57948641	0.86[ASN][1000 genomes]
rs58297927	0.86[ASN][1000 genomes]
rs58483300	0.84[ASN][1000 genomes]
rs59111239	0.89[ASN][1000 genomes]
rs59421055	0.82[ASN][1000 genomes]
rs59504156	0.85[ASN][1000 genomes]
rs60642012	0.82[ASN][1000 genomes]
rs60670838	0.87[ASN][1000 genomes]
rs60733259	0.84[ASN][1000 genomes]
rs6433670	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6433673	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6710575	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6742951	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7565022	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7573763	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7586051	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587604	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7591807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7604673	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7606235	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7607450	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8941	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs952746	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9679607	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9789582	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2060929	TTC30B	cis	parietal	SCAN
rs2060929	DKFZp451M2119	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178258800-178285000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:178258800-178294200	Weak transcription	Thymus	Thymus
3	chr2:178260200-178280200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:178260400-178285600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:178263400-178291800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr2:178264200-178282800	Weak transcription	Dnd41	blood
7	chr2:178264200-178291600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:178264400-178280400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:178265600-178287000	Weak transcription	K562	blood
10	chr2:178266000-178280200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:178269200-178283000	Weak transcription	HSMM	muscle
12	chr2:178269200-178283000	Weak transcription	Osteobl	bone
13	chr2:178270000-178280200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:178270200-178280800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:178270400-178281000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:178270400-178281000	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:178270400-178294400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:178271800-178291600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:178272400-178285600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr2:178272800-178295200	Weak transcription	Left Ventricle	heart
21	chr2:178273000-178288800	Weak transcription	GM12878-XiMat	blood
22	chr2:178273400-178286600	Weak transcription	HSMMtube	muscle
23	chr2:178273400-178288600	Weak transcription	Primary T cells from cord blood	blood
24	chr2:178274400-178282800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:178274600-178280400	Weak transcription	Fetal Intestine Small	intestine
26	chr2:178274600-178291800	Weak transcription	Primary B cells from cord blood	blood
27	chr2:178276400-178291400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:178276800-178289800	Weak transcription	Fetal Intestine Large	intestine
29	chr2:178276800-178294400	Weak transcription	Psoas Muscle	Psoas
30	chr2:178277400-178291800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:178277800-178280600	Weak transcription	Fetal Stomach	stomach
32	chr2:178278000-178285400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:178278200-178285000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:178278400-178280800	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:178278600-178282800	Weak transcription	A549	lung
36	chr2:178278800-178281000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:178278800-178282600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:178278800-178282800	Weak transcription	NHEK	skin
39	chr2:178278800-178283000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:178278800-178283600	Weak transcription	HMEC	breast
41	chr2:178279200-178283600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:178279600-178294400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:178279800-178280600	Enhancers	Hela-S3	cervix
44	chr2:178279800-178280800	Enhancers	HepG2	liver
45	chr2:178279800-178281000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:178279800-178281400	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr2:178279800-178284200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:178280000-178280200	Enhancers	Fetal Lung	lung
49	chr2:178280000-178280400	Enhancers	Small Intestine	intestine
50	chr2:178280000-178281000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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