Variant report

Variant	rs9941681
Chromosome Location	chr2:178209345-178209346
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	chr2:178208196..178211847-chr2:178255899..178258427,3	K562	blood:
2	chr2:178207678..178210773-chr2:178255899..178258732,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AGPS-4	chr2:178209171-178209564	NONHSAT075718

Variant related genes	Relation type
ENSG00000213963	Chromatin interaction
ENSG00000018510	Chromatin interaction
ENSG00000116044	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10172305	1.00[ASN][1000 genomes]
rs10173008	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173172	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176724	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs10179735	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179975	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs10184488	0.92[GIH][hapmap]
rs10196753	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196915	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207932	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs10497509	0.92[GIH][hapmap]
rs10497510	1.00[ASN][1000 genomes]
rs10803912	0.92[GIH][hapmap]
rs10930784	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs10930785	0.85[ASW][hapmap];0.94[CEU][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10930786	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930789	1.00[ASN][1000 genomes]
rs11889478	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468046	1.00[CHD][hapmap];0.92[GIH][hapmap]
rs12621156	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[ASN][1000 genomes]
rs12623239	0.89[CEU][hapmap]
rs12693118	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693119	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987686	0.94[CEU][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap]
rs13001890	0.89[CEU][hapmap]
rs13002088	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs1349762	1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[ASN][1000 genomes]
rs1377491	0.89[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs1453369	1.00[ASN][1000 genomes]
rs1453376	0.89[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463287	1.00[ASN][1000 genomes]
rs1463288	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs1466208	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs1551287	1.00[ASN][1000 genomes]
rs1551288	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs1551289	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs1551290	1.00[ASN][1000 genomes]
rs1584806	1.00[ASN][1000 genomes]
rs1597959	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs17326999	1.00[CHD][hapmap];0.92[GIH][hapmap]
rs17648502	1.00[ASN][1000 genomes]
rs1869357	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1901828	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs1973045	1.00[ASN][1000 genomes]
rs2084966	1.00[ASN][1000 genomes]
rs2123641	1.00[ASN][1000 genomes]
rs2123643	1.00[ASN][1000 genomes]
rs2123644	1.00[ASN][1000 genomes]
rs2123645	1.00[ASN][1000 genomes]
rs2167902	0.92[GIH][hapmap]
rs2167903	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2167904	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs2178017	1.00[CHD][hapmap];0.92[GIH][hapmap]
rs2293475	0.92[GIH][hapmap]
rs2364733	0.89[CEU][hapmap]
rs2364846	1.00[ASN][1000 genomes]
rs2364847	0.94[CEU][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364848	0.94[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2364849	1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[ASN][1000 genomes]
rs2364850	1.00[ASN][1000 genomes]
rs2364851	0.91[GIH][hapmap]
rs2444563	0.84[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs2444564	1.00[ASN][1000 genomes]
rs2464655	1.00[ASN][1000 genomes]
rs2602527	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs2602528	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs2706143	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs2706144	1.00[ASN][1000 genomes]
rs2706145	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs2706146	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs2706147	0.89[CEU][hapmap]
rs2706150	1.00[ASN][1000 genomes]
rs2706153	1.00[ASN][1000 genomes]
rs2706154	1.00[ASN][1000 genomes]
rs2706155	1.00[ASN][1000 genomes]
rs2706156	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs2706157	1.00[ASN][1000 genomes]
rs2706158	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs2706162	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs2706163	1.00[ASN][1000 genomes]
rs3754989	0.92[GIH][hapmap]
rs3952496	1.00[ASN][1000 genomes]
rs4130304	0.94[CEU][hapmap]
rs4350784	0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs4402804	0.92[GIH][hapmap]
rs4893826	1.00[ASN][1000 genomes]
rs4893827	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs4893829	0.92[GIH][hapmap]
rs4893930	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs4893933	1.00[ASN][1000 genomes]
rs4893955	0.84[GIH][hapmap]
rs56951837	1.00[ASN][1000 genomes]
rs6414095	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs6433661	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433662	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433672	1.00[CHD][hapmap];0.84[GIH][hapmap]
rs6719278	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720483	1.00[CHD][hapmap];0.92[GIH][hapmap]
rs6721168	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs6732113	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732250	0.84[GIH][hapmap]
rs6732256	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739792	1.00[ASN][1000 genomes]
rs6741974	1.00[ASN][1000 genomes]
rs6754660	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs72946169	1.00[ASN][1000 genomes]
rs7559715	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs7566603	1.00[ASN][1000 genomes]
rs7566686	1.00[ASN][1000 genomes]
rs7573334	1.00[ASN][1000 genomes]
rs7573583	0.89[CEU][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs7575328	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs7588049	0.91[GIH][hapmap]
rs7588444	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594073	0.92[GIH][hapmap]
rs7604299	0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs7608135	0.92[GIH][hapmap]
rs9288001	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs952034	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs9917333	1.00[ASN][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	nsv3051	chr2:178193436-178239394	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9941681	DKFZp451M2119	cis	multi-tissue	Pritchard

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178187600-178216400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:178187800-178210800	Weak transcription	Left Ventricle	heart
3	chr2:178187800-178216400	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:178195200-178213600	Weak transcription	Gastric	stomach
5	chr2:178195400-178211400	Weak transcription	Fetal Intestine Small	intestine
6	chr2:178197200-178211800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:178197200-178211800	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:178197200-178212000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:178197200-178213400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:178197200-178215000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:178197200-178216800	Weak transcription	Primary T cells from cord blood	blood
12	chr2:178197200-178217600	Weak transcription	Primary B cells from cord blood	blood
13	chr2:178197600-178211200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:178197600-178217200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:178197800-178211400	Weak transcription	Fetal Heart	heart
16	chr2:178197800-178214000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:178197800-178215400	Weak transcription	Dnd41	blood
18	chr2:178198000-178210600	Weak transcription	HepG2	liver
19	chr2:178198000-178213000	Weak transcription	Ovary	ovary
20	chr2:178199000-178214400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr2:178199600-178213600	Weak transcription	Brain Angular Gyrus	brain
22	chr2:178200800-178213600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:178201000-178211000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:178201000-178211200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:178202200-178217400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:178203200-178216400	Weak transcription	HSMMtube	muscle
27	chr2:178203200-178217800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:178203400-178210400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:178203400-178215000	Weak transcription	Adipose Nuclei	Adipose
30	chr2:178203400-178216000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:178203400-178216000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:178203400-178217000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:178203400-178244400	Weak transcription	HSMM	muscle
34	chr2:178203600-178213000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:178203800-178214000	Weak transcription	K562	blood
36	chr2:178203800-178221600	Weak transcription	A549	lung
37	chr2:178207000-178210800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:178208400-178209600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:178208800-178214200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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