Variant report

Variant	rs253414
Chromosome Location	chr5:74956517-74956518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:74950997..74952941-chr5:74954987..74957253,2	K562	blood:
2	chr5:74955921..74958847-chr5:74961478..74964262,3	K562	blood:
3	chr5:74953873..74956590-chr5:75014538..75016068,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10057967	0.85[MEX][hapmap]
rs253391	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs253411	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs253412	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34351	0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34358	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34359	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34360	0.96[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34361	0.96[CEU][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3797580	0.85[MEX][hapmap]
rs40060	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs42302	0.90[CEU][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4549504	0.82[GIH][hapmap]
rs4604177	0.82[GIH][hapmap]
rs5744680	0.84[GIH][hapmap]
rs6892146	0.83[ASW][hapmap];0.92[YRI][hapmap]
rs888787	0.80[AFR][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	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv522003	chr5:74947435-74988369	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs253414	DMGDH	cis	parietal	SCAN
rs253414	ANKRA2	cis	cerebellum	SCAN
rs253414	TNPO1	cis	cerebellum	SCAN
rs253414	HMGCR	cis	parietal	SCAN
rs253414	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74921800-74964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:74945000-74962800	Weak transcription	Fetal Intestine Large	intestine
3	chr5:74948000-74959200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:74952400-74957800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:74952600-74964200	Weak transcription	Stomach Mucosa	stomach
6	chr5:74952800-74957200	Weak transcription	Brain Germinal Matrix	brain
7	chr5:74952800-74957400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:74952800-74957400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:74952800-74958000	Weak transcription	Fetal Brain Male	brain
10	chr5:74952800-74959200	Weak transcription	Fetal Intestine Small	intestine
11	chr5:74952800-74964000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr5:74952800-74964200	Weak transcription	Right Ventricle	heart
13	chr5:74952800-74964400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:74952800-74981400	Weak transcription	Psoas Muscle	Psoas
15	chr5:74953000-74957400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:74953000-74958000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:74953000-74959000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:74953000-74959200	Weak transcription	Brain Substantia Nigra	brain
19	chr5:74953000-74961000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:74953000-74964200	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:74953000-74964400	Weak transcription	Adipose Nuclei	Adipose
22	chr5:74953000-74964400	Weak transcription	Fetal Kidney	kidney
23	chr5:74953000-74964400	Weak transcription	Fetal Stomach	stomach
24	chr5:74953000-74964600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:74954400-74958000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:74955000-74956800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:74955000-74957200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr5:74955600-74956800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr5:74956000-74956800	Flanking Active TSS	GM12878-XiMat	blood
30	chr5:74956000-74965000	Weak transcription	NHEK	skin
31	chr5:74956200-74956600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr5:74956200-74956600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr5:74956200-74957400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:74956400-74956800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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