Variant report

Variant	rs2297850
Chromosome Location	chr1:47042612-47042613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:47042570-47042664	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47041717..47044206-chr1:47067000..47069818,2	K562	blood:
2	chr1:47041661..47043778-chr1:47070091..47072496,2	K562	blood:
3	chr1:47038566..47040285-chr1:47040736..47042855,2	K562	blood:

Variant related genes	Relation type
MKNK1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10890406	0.93[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes]
rs10890408	0.93[CEU][hapmap]
rs11211319	0.92[CEU][hapmap];0.96[TSI][hapmap]
rs11211324	0.93[CEU][hapmap];0.83[AMR][1000 genomes]
rs11211325	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs11211326	0.87[AMR][1000 genomes]
rs12022855	0.93[CEU][hapmap];0.98[TSI][hapmap]
rs1258012	0.93[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes]
rs17102321	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs35494693	0.91[AMR][1000 genomes]
rs36058295	0.81[AMR][1000 genomes]
rs4275405	0.91[CEU][hapmap]
rs4660357	0.93[CEU][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs4660947	0.86[AMR][1000 genomes]
rs6671527	0.85[CEU][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap]
rs6687832	0.82[AMR][1000 genomes]
rs6704020	0.87[AMR][1000 genomes]
rs7526249	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7526328	0.94[AMR][1000 genomes]
rs942083	0.93[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes]
rs956526	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs956527	0.93[CEU][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1009899	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv534954	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv1011892	chr1:47010519-47067492	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2297850	MMACHC	cis	cerebellum	SCAN
rs2297850	FAM183A	cis	cerebellum	SCAN
rs2297850	CCDC23	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47015800-47043400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:47019800-47043600	Weak transcription	Dnd41	blood
3	chr1:47020800-47047400	Weak transcription	Brain Germinal Matrix	brain
4	chr1:47021000-47057000	Weak transcription	Fetal Brain Male	brain
5	chr1:47021200-47045000	Weak transcription	K562	blood
6	chr1:47021800-47054600	Weak transcription	A549	lung
7	chr1:47022200-47043400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:47022400-47053600	Strong transcription	Thymus	Thymus
9	chr1:47022600-47051400	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:47022600-47051600	Strong transcription	Liver	Liver
11	chr1:47023000-47044200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:47023000-47047400	Strong transcription	Primary T cells from cord blood	blood
13	chr1:47023200-47044400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr1:47023200-47046600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:47023200-47047200	Strong transcription	Fetal Thymus	thymus
16	chr1:47023200-47051200	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:47023200-47060000	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:47023400-47044600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:47023800-47045200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:47023800-47053200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:47024000-47054800	Weak transcription	HUVEC	blood vessel
22	chr1:47025600-47062400	Weak transcription	Fetal Heart	heart
23	chr1:47027200-47047600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:47027600-47043400	Weak transcription	HepG2	liver
25	chr1:47028800-47043600	Weak transcription	HMEC	breast
26	chr1:47028800-47044800	Weak transcription	Stomach Mucosa	stomach
27	chr1:47030800-47046000	Weak transcription	Psoas Muscle	Psoas
28	chr1:47031200-47045600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:47031400-47043400	Weak transcription	Osteobl	bone
30	chr1:47032600-47046200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:47033200-47043000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:47034200-47044800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:47035200-47044800	Strong transcription	Placenta	Placenta
34	chr1:47035200-47047600	Weak transcription	NHDF-Ad	bronchial
35	chr1:47035200-47048000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr1:47035200-47053000	Strong transcription	Spleen	Spleen
37	chr1:47035600-47053400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr1:47036000-47047400	Weak transcription	Fetal Lung	lung
39	chr1:47036000-47056400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:47036000-47060000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:47036200-47045000	Weak transcription	Fetal Kidney	kidney
42	chr1:47036400-47053200	Strong transcription	Fetal Stomach	stomach
43	chr1:47036600-47045600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:47037000-47046400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:47037800-47047400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:47037800-47057000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:47038400-47053200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:47038600-47050800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr1:47039000-47042800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:47039000-47043000	Strong transcription	Primary B cells from cord blood	blood

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