Variant report

Variant	rs912768
Chromosome Location	chr1:173473713-173473714
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173445909..173448174-chr1:173472992..173475545,2	MCF-7	breast:
2	chr1:173471541..173474738-chr1:173476002..173477727,3	MCF-7	breast:
3	chr1:173455943..173458874-chr1:173472089..173474445,2	MCF-7	breast:
4	chr1:173444700..173449124-chr1:173472471..173476984,5	MCF-7	breast:
5	chr1:173454021..173455524-chr1:173471878..173474498,2	K562	blood:
6	chr1:173445753..173447978-chr1:173472675..173475693,4	K562	blood:

Variant related genes	Relation type
ENSG00000117592	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10753082	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753083	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912633	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912650	0.84[AMR][1000 genomes]
rs12075314	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080722	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359460	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461022	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461024	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461025	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1547154	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570813	0.82[AMR][1000 genomes]
rs1886638	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382766	0.85[LWK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs4405161	1.00[JPT][hapmap]
rs4472784	1.00[JPT][hapmap]
rs4573551	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4611	0.82[AFR][1000 genomes]
rs4916366	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916367	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916371	0.82[AMR][1000 genomes]
rs7314	0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs7535963	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540065	0.88[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs7551305	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425411	1.00[JPT][hapmap];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs912768	RABGAP1L	cis	lymphoblastoid	seeQTL
rs912768	TNFSF4	cis	parietal	SCAN
rs912768	DARS2	cis	cerebellum	SCAN
rs912768	PRDX6	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173448000-173477000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:173458600-173475600	Weak transcription	Fetal Kidney	kidney
3	chr1:173458600-173476600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:173459400-173474000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:173459400-173475400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:173466400-173475400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:173471000-173474200	Enhancers	Liver	Liver
8	chr1:173472400-173473800	Enhancers	Adipose Nuclei	Adipose
9	chr1:173472400-173474000	Enhancers	Stomach Smooth Muscle	stomach
10	chr1:173472600-173473800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:173472600-173474000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:173472800-173473800	Enhancers	Stomach Mucosa	stomach
13	chr1:173472800-173474800	Weak transcription	HSMMtube	muscle
14	chr1:173472800-173475400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:173473000-173473800	Flanking Active TSS	Hela-S3	cervix
16	chr1:173473000-173474000	Enhancers	Fetal Brain Female	brain
17	chr1:173473200-173475400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:173473200-173475800	Weak transcription	NHLF	lung
19	chr1:173473200-173476200	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:173473200-173476200	Weak transcription	K562	blood
21	chr1:173473200-173476600	Weak transcription	NHDF-Ad	bronchial
22	chr1:173473400-173475600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:173473600-173474000	Weak transcription	Fetal Brain Male	brain
24	chr1:173473600-173476600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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