Variant report

Variant	rs2759385
Chromosome Location	chr6:163844597-163844598
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163842546..163846148-chr6:163847006..163850145,4	K562	blood:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1003528	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1016501	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1016502	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1040514	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1047944	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752044	1.00[ASN][1000 genomes]
rs12194023	1.00[ASN][1000 genomes]
rs1230321	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234603	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1234604	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1234976	1.00[ASN][1000 genomes]
rs1614795	1.00[ASN][1000 genomes]
rs1619076	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1619863	1.00[ASN][1000 genomes]
rs1629251	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737317	1.00[CHB][hapmap]
rs1737323	1.00[CHB][hapmap]
rs1737329	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737333	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737600	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737601	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737603	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737604	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737606	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737607	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737609	1.00[ASN][1000 genomes]
rs1737611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737612	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744924	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1744925	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1744926	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[ASN][1000 genomes]
rs1744927	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1744928	1.00[ASN][1000 genomes]
rs1744933	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1745094	0.92[CEU][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764008	1.00[CHB][hapmap]
rs2038146	1.00[ASN][1000 genomes]
rs2038147	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2057003	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2092406	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2092407	1.00[ASN][1000 genomes]
rs2179523	1.00[ASN][1000 genomes]
rs2179524	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[ASN][1000 genomes]
rs2321698	1.00[ASN][1000 genomes]
rs2321700	1.00[ASN][1000 genomes]
rs2321701	0.88[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2321702	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2484877	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744420	1.00[ASN][1000 genomes]
rs2744421	1.00[ASN][1000 genomes]
rs2745364	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2745365	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757578	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2757579	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757581	1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757582	1.00[ASN][1000 genomes]
rs2757583	1.00[ASN][1000 genomes]
rs2757586	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2757587	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2757588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2757589	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759381	1.00[ASN][1000 genomes]
rs2759383	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759384	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759387	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759389	1.00[ASN][1000 genomes]
rs2759390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759391	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759392	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759393	1.00[ASN][1000 genomes]
rs2759395	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759398	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759399	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2784865	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2784867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2784873	1.00[ASN][1000 genomes]
rs2784874	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap]
rs2874602	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4708996	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708997	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs5008180	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56721804	1.00[ASN][1000 genomes]
rs6455900	1.00[ASN][1000 genomes]
rs6455902	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6455903	1.00[ASN][1000 genomes]
rs6455904	1.00[ASN][1000 genomes]
rs6909364	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6913113	1.00[ASN][1000 genomes]
rs6914387	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6915247	1.00[ASN][1000 genomes]
rs6924130	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6926584	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6927417	1.00[ASN][1000 genomes]
rs6931049	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs721190	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs721191	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7746116	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749189	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7752945	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7761088	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7768051	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7769145	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7775850	1.00[ASN][1000 genomes]
rs7776279	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs783136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783138	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs783140	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs803613	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs809155	1.00[ASN][1000 genomes]
rs813640	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814143	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9295222	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9295223	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[ASN][1000 genomes]
rs9295224	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs9347754	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9347755	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9347756	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9347759	1.00[ASN][1000 genomes]
rs9347763	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355427	1.00[CHB][hapmap]
rs9356117	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9356119	1.00[CHB][hapmap]
rs9356120	1.00[ASN][1000 genomes]
rs9356121	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365572	1.00[ASN][1000 genomes]
rs9365573	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9365574	1.00[ASN][1000 genomes]
rs9365577	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365578	0.81[CEU][hapmap]
rs9456866	1.00[ASN][1000 genomes]
rs9456869	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2759385	MTHFS	trans	lymphoblastoid	seeQTL
rs2759385	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163837400-163857200	Weak transcription	Spleen	Spleen
2	chr6:163837800-163851000	Weak transcription	Small Intestine	intestine
3	chr6:163838000-163847600	Weak transcription	Pancreas	Pancrea
4	chr6:163838000-163851600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:163838000-163860600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:163838400-163845000	Weak transcription	Placenta	Placenta
7	chr6:163838800-163845200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:163839200-163845400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:163839600-163846200	Weak transcription	Thymus	Thymus
10	chr6:163839800-163851600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:163840000-163845000	Enhancers	Colon Smooth Muscle	Colon
12	chr6:163840200-163844800	Weak transcription	Hela-S3	cervix
13	chr6:163840200-163844800	Enhancers	HepG2	liver
14	chr6:163840800-163865000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:163840800-163881400	Weak transcription	Fetal Stomach	stomach
16	chr6:163841000-163847600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:163841600-163845800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:163841600-163847400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:163841600-163847400	Weak transcription	Aorta	Aorta
20	chr6:163841600-163848000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:163841600-163848600	Weak transcription	HMEC	breast
22	chr6:163841600-163853200	Enhancers	Adipose Nuclei	Adipose
23	chr6:163841600-163858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:163841600-163864400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:163841800-163845600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:163841800-163848600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:163841800-163851000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:163842000-163844600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:163842000-163845200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:163842000-163846000	Weak transcription	Stomach Mucosa	stomach
31	chr6:163842000-163847600	Enhancers	Fetal Brain Male	brain
32	chr6:163842000-163848200	Weak transcription	GM12878-XiMat	blood
33	chr6:163842000-163850000	Weak transcription	HSMMtube	muscle
34	chr6:163842200-163851000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:163842400-163844600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:163842400-163847200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:163842400-163848000	Weak transcription	Fetal Lung	lung
38	chr6:163842400-163849800	Weak transcription	Primary T cells from cord blood	blood
39	chr6:163842600-163845400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:163842600-163847400	Weak transcription	HUVEC	blood vessel
41	chr6:163842600-163865200	Weak transcription	Fetal Kidney	kidney
42	chr6:163842800-163846400	Enhancers	Ovary	ovary
43	chr6:163843000-163844800	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr6:163843000-163845600	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr6:163843000-163845800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr6:163843000-163846600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr6:163843200-163845400	Genic enhancers	Fetal Muscle Leg	muscle
48	chr6:163843200-163848600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr6:163843400-163844600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:163843400-163844600	Enhancers	HUES6 Cell Line	embryonic stem cell

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