Variant report

Variant	rs7561242
Chromosome Location	chr2:74466152-74466153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74427072..74428786-chr2:74464824..74466711,2	K562	blood:
2	chr2:74457826..74461318-chr2:74461527..74466761,7	K562	blood:
3	chr2:74465067..74466626-chr2:74486160..74488406,2	MCF-7	breast:
4	chr2:74447215..74450146-chr2:74463449..74466578,3	K562	blood:
5	chr2:74458595..74460503-chr2:74464982..74467627,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13024188	0.81[EUR][1000 genomes]
rs2034454	0.95[JPT][hapmap]
rs6546896	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs6731545	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7558047	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7571842	0.94[CHD][hapmap];0.95[JPT][hapmap]
rs895987	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs895988	0.94[CHD][hapmap];0.95[JPT][hapmap]

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
rs7561242	MTHFD2	cis	lymphoblastoid	seeQTL
rs7561242	TTC31	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74427400-74484400	Weak transcription	Fetal Lung	lung
2	chr2:74427800-74494200	Weak transcription	Brain Germinal Matrix	brain
3	chr2:74439800-74525200	Weak transcription	Fetal Brain Male	brain
4	chr2:74441800-74490400	Weak transcription	Fetal Brain Female	brain
5	chr2:74442400-74477400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr2:74444800-74494200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:74448800-74494000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:74449200-74470600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:74449200-74502200	Weak transcription	Spleen	Spleen
10	chr2:74449400-74494000	Weak transcription	Primary T cells from cord blood	blood
11	chr2:74449400-74507000	Weak transcription	Brain Anterior Caudate	brain
12	chr2:74450000-74494000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:74454200-74508200	Weak transcription	Ovary	ovary
14	chr2:74454400-74466200	Weak transcription	Esophagus	oesophagus
15	chr2:74454400-74470200	Weak transcription	Gastric	stomach
16	chr2:74454400-74471800	Weak transcription	Psoas Muscle	Psoas
17	chr2:74454400-74474200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:74455400-74469600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:74455400-74469800	Weak transcription	Left Ventricle	heart
20	chr2:74455400-74470200	Weak transcription	Right Ventricle	heart
21	chr2:74455400-74473600	Weak transcription	Lung	lung
22	chr2:74455600-74480000	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:74458600-74483400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:74458800-74488200	Weak transcription	Pancreas	Pancrea
25	chr2:74461800-74474000	Weak transcription	Fetal Stomach	stomach
26	chr2:74462200-74494000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:74462400-74493800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:74462600-74473600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:74462600-74509600	Weak transcription	Brain Substantia Nigra	brain
30	chr2:74462800-74467000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:74462800-74469600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:74462800-74473200	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:74462800-74473400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:74463000-74544800	Weak transcription	Brain Angular Gyrus	brain
35	chr2:74463400-74473000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:74464200-74469600	Weak transcription	Hela-S3	cervix
37	chr2:74465800-74466800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:74466000-74466200	ZNF genes & repeats	Adipose Nuclei	Adipose

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