Variant report

Variant	rs895988
Chromosome Location	chr2:74461634-74461635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74460638..74463083-chr4:67494064..67495854,2	MCF-7	breast:
2	chr2:74457826..74461318-chr2:74461527..74466761,7	K562	blood:
3	chr2:74424696..74427673-chr2:74460558..74464630,6	MCF-7	breast:
4	chr2:74457826..74461075-chr2:74461527..74464148,4	K562	blood:

Variant related genes	Relation type
ENSG00000065911	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10177833	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1667627	0.82[GIH][hapmap]
rs2001802	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2034454	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546896	0.91[JPT][hapmap]
rs702465	0.83[MEX][hapmap]
rs7561242	0.94[CHD][hapmap];0.95[JPT][hapmap]
rs7571842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583544	0.81[AMR][1000 genomes];0.85[EUR][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	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
2	nsv834261	chr2:74391709-74613720	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3401140	chr2:74439333-74533696	Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv3380034	chr2:74439354-74533666	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs895988	MTHFD2	cis	lymphoblastoid	seeQTL
rs895988	MOBK1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74427400-74462000	Weak transcription	Brain Angular Gyrus	brain
2	chr2:74427400-74484400	Weak transcription	Fetal Lung	lung
3	chr2:74427800-74494200	Weak transcription	Brain Germinal Matrix	brain
4	chr2:74433800-74461800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:74439800-74525200	Weak transcription	Fetal Brain Male	brain
6	chr2:74441800-74466000	Weak transcription	Adipose Nuclei	Adipose
7	chr2:74441800-74490400	Weak transcription	Fetal Brain Female	brain
8	chr2:74442400-74477400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:74442800-74465200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr2:74444800-74494200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:74447400-74463000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:74448800-74494000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:74449200-74465200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:74449200-74470600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:74449200-74502200	Weak transcription	Spleen	Spleen
16	chr2:74449400-74494000	Weak transcription	Primary T cells from cord blood	blood
17	chr2:74449400-74507000	Weak transcription	Brain Anterior Caudate	brain
18	chr2:74449600-74462000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:74450000-74494000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:74453800-74465800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:74454200-74508200	Weak transcription	Ovary	ovary
22	chr2:74454400-74466200	Weak transcription	Esophagus	oesophagus
23	chr2:74454400-74470200	Weak transcription	Gastric	stomach
24	chr2:74454400-74471800	Weak transcription	Psoas Muscle	Psoas
25	chr2:74454400-74474200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:74454800-74462000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:74455400-74464800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:74455400-74469600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:74455400-74469800	Weak transcription	Left Ventricle	heart
30	chr2:74455400-74470200	Weak transcription	Right Ventricle	heart
31	chr2:74455400-74473600	Weak transcription	Lung	lung
32	chr2:74455600-74463400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:74455600-74480000	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:74458000-74461800	Strong transcription	Fetal Stomach	stomach
35	chr2:74458200-74463400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:74458600-74483400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:74458800-74488200	Weak transcription	Pancreas	Pancrea
38	chr2:74459200-74462800	Strong transcription	Brain Hippocampus Middle	brain
39	chr2:74460200-74462600	Strong transcription	Brain Substantia Nigra	brain
40	chr2:74460400-74462000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:74461600-74462800	Strong transcription	Brain Inferior Temporal Lobe	brain

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