Variant report

Variant	rs16847730
Chromosome Location	chr1:174994790-174994791
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174992317..174994032-chr1:174994070..174996061,2	K562	blood:
2	chr1:174992825..174995632-chr1:174996081..174999511,5	MCF-7	breast:
3	chr1:174965007..174966867-chr1:174993864..174995754,2	MCF-7	breast:
4	chr1:174994289..174996013-chr1:175298978..175301005,2	K562	blood:

Variant related genes	Relation type
ENSG00000252552	Chromatin interaction
ENSG00000120333	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10489330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10489332	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11811190	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12140378	0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12735946	0.81[EUR][1000 genomes]
rs12737503	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2861102	0.93[ASN][1000 genomes]
rs2861106	0.85[CEU][hapmap];0.88[CHB][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs35035962	0.81[EUR][1000 genomes]
rs35464086	0.80[EUR][1000 genomes]
rs3737935	0.80[EUR][1000 genomes]
rs3753562	0.80[AFR][1000 genomes]
rs41266060	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41266064	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41498747	0.88[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs57053120	0.80[AFR][1000 genomes]
rs58618779	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58762254	0.84[AFR][1000 genomes]
rs60893569	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688577	0.85[YRI][hapmap]
rs6700434	0.88[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv947512	chr1:174984818-175000909	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	esv3395419	chr1:174994329-174997427	Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv3423951	chr1:174994554-174997102	Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16847730	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL
rs16847730	C1orf156	cis	parietal	SCAN
rs16847730	RABGAP1L	cis	normal skin	skin_eQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174993200-174995200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:174993200-174998200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:174993200-174998200	Weak transcription	Fetal Intestine Large	intestine
4	chr1:174993200-174998200	Weak transcription	HMEC	breast
5	chr1:174993200-174998400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:174993200-174998400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr1:174993200-174998600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:174993200-174998600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:174993200-174998600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:174993200-174998600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr1:174993200-174998800	Weak transcription	Adipose Nuclei	Adipose
12	chr1:174993200-174998800	Weak transcription	Brain Substantia Nigra	brain
13	chr1:174993200-175004800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:174993200-175013800	Weak transcription	Spleen	Spleen
15	chr1:174993400-174998200	Weak transcription	Fetal Intestine Small	intestine
16	chr1:174993400-174998200	Weak transcription	Pancreas	Pancrea
17	chr1:174993400-174998200	Weak transcription	HepG2	liver
18	chr1:174993400-174998400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:174993400-174998600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:174993400-174998600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:174993400-174998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:174993400-174998600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:174993400-174998600	Weak transcription	Fetal Thymus	thymus
24	chr1:174993400-174998600	Weak transcription	K562	blood
25	chr1:174993400-174998800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:174993600-174998600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr1:174993600-174998600	Weak transcription	Dnd41	blood

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