Variant report

Variant	rs10504311
Chromosome Location	chr8:61309122-61309123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:60964154..60965120-chr8:61309098..61310160,4	K562	blood:
2	chr8:61145703..61146486-chr8:61308857..61310218,7	K562	blood:
3	chr8:61145523..61146919-chr8:61308664..61310037,8	MCF-7	breast:
4	chr8:61304106..61306671-chr8:61306892..61309869,2	K562	blood:
5	chr8:61192430..61196351-chr8:61307974..61311506,6	K562	blood:
6	chr8:61191411..61194665-chr8:61308206..61311022,3	K562	blood:
7	chr8:61181201..61184970-chr8:61306411..61309605,3	K562	blood:

Variant related genes	Relation type
ENSG00000178538	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10100740	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10101576	0.82[ASN][1000 genomes]
rs10101714	0.87[ASN][1000 genomes]
rs10109278	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap]
rs10957135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs10957136	0.93[ASN][1000 genomes]
rs10957137	0.87[ASN][1000 genomes]
rs10957138	0.82[ASN][1000 genomes]
rs10957140	0.82[ASN][1000 genomes]
rs10957141	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.81[ASN][1000 genomes]
rs10957146	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap]
rs10957149	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11774500	0.81[ASN][1000 genomes]
rs11775407	0.97[ASN][1000 genomes]
rs11778529	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11778708	0.81[ASN][1000 genomes]
rs11778772	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11778888	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11782178	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap]
rs11782463	0.81[ASN][1000 genomes]
rs11784284	0.81[ASN][1000 genomes]
rs11988528	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12678694	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap]
rs13266707	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13267828	0.87[ASN][1000 genomes]
rs13269925	0.81[ASN][1000 genomes]
rs1480342	0.93[ASN][1000 genomes]
rs2326556	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.96[ASN][1000 genomes]
rs2326557	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.96[ASN][1000 genomes]
rs28405386	0.98[ASN][1000 genomes]
rs28542403	0.80[ASN][1000 genomes]
rs28678079	0.81[ASN][1000 genomes]
rs2875966	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs34775344	0.81[ASN][1000 genomes]
rs35837434	0.81[ASN][1000 genomes]
rs6471883	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6471884	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6987523	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6991529	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6993237	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6995397	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs6996344	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6998294	0.87[ASN][1000 genomes]
rs7017556	0.98[ASN][1000 genomes]
rs7357376	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7820349	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7822391	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7826226	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7832664	0.90[ASN][1000 genomes]
rs7832964	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7842105	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[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	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1022752	chr8:61095248-61322302	Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3371465	chr8:61115030-61356658	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv831334	chr8:61148796-61330190	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10504311	LOC643763	cis	parietal	SCAN
rs10504311	RAB2	cis	lesional skin	skin_eQTL
rs10504311	RAB2	cis	uninvolved skin	skin_eQTL
rs10504311	RAB2A	Cis_1M	lymphoblastoid	RTeQTL
rs10504311	RAB2	cis	normal skin	skin_eQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61305800-61310000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr8:61308000-61309200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr8:61308200-61310000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr8:61308400-61309200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:61308400-61309600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr8:61308400-61309600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr8:61308600-61309200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr8:61308600-61309200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:61308600-61309200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr8:61308600-61309200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr8:61308600-61309400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr8:61308600-61309400	Enhancers	Rectal Smooth Muscle	rectum
13	chr8:61308600-61309600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr8:61308600-61309800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:61308800-61309400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr8:61308800-61309400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr8:61308800-61309400	Enhancers	Colon Smooth Muscle	Colon
18	chr8:61308800-61309400	Enhancers	Fetal Heart	heart
19	chr8:61308800-61309400	Enhancers	Fetal Kidney	kidney
20	chr8:61308800-61309400	Enhancers	Fetal Lung	lung
21	chr8:61308800-61309800	Enhancers	Brain Germinal Matrix	brain
22	chr8:61308800-61310000	Enhancers	Brain Hippocampus Middle	brain
23	chr8:61308800-61310000	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr8:61308800-61310000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr8:61308800-61310000	Enhancers	Stomach Smooth Muscle	stomach
26	chr8:61309000-61309400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr8:61309000-61311800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr8:61309000-61315200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr8:61309000-61330000	Weak transcription	Right Atrium	heart

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