Variant report

Variant	rs912767
Chromosome Location	chr1:173456445-173456446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173454886..173456981-chr1:173791612..173793334,2	K562	blood:
2	chr1:173456168..173461242-chr1:173467676..173473413,6	K562	blood:
3	chr1:173398971..173403137-chr1:173453478..173457136,4	K562	blood:
4	chr1:173446558..173448990-chr1:173454032..173456674,3	MCF-7	breast:
5	chr1:173455943..173458874-chr1:173472089..173474445,2	MCF-7	breast:
6	chr1:173454680..173459783-chr1:173793534..173797579,4	K562	blood:
7	chr1:173450429..173453929-chr1:173454032..173458436,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120334	Chromatin interaction
ENSG00000117593	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10737301	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs10753078	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10753079	0.86[EUR][1000 genomes]
rs10753080	0.86[EUR][1000 genomes]
rs10798290	0.80[CHB][hapmap]
rs10912624	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10912626	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10912627	0.82[LWK][hapmap]
rs10912641	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10912643	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs12026427	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs12026677	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs12037210	1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs12039524	0.88[CEU][hapmap]
rs12058528	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12065426	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12077271	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12080769	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12565753	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12724371	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12744504	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12745058	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12753631	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12760501	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1461014	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1886639	1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs33942654	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33951697	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34025182	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34259759	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34296122	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34331061	0.87[EUR][1000 genomes]
rs34332254	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34919111	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34931189	0.82[ASN][1000 genomes]
rs35065145	0.85[ASN][1000 genomes]
rs35379498	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35607505	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35632090	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35831548	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35845062	0.87[EUR][1000 genomes]
rs36058163	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3934575	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs3934576	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs4244195	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs4244196	0.86[EUR][1000 genomes]
rs4294450	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs4310474	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs4462186	0.87[EUR][1000 genomes]
rs4539167	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57032935	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826747	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61826748	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61826749	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61826753	0.86[ASN][1000 genomes]
rs61828886	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61828887	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61828888	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425232	0.87[EUR][1000 genomes]
rs6425251	0.80[CHB][hapmap]
rs6660804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66683313	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6670071	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6671141	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6687872	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6696443	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6699094	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs68193118	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7314	0.83[MEX][hapmap]
rs7413754	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516544	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7520641	0.86[EUR][1000 genomes]
rs7521536	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524403	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7529089	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529377	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7530469	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7540065	0.83[MEX][hapmap]
rs7541082	0.80[CHB][hapmap]
rs7549074	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv947335	chr1:173455122-173458140	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs912767	PRDX6	cis	parietal	SCAN
rs912767	GORAB	cis	parietal	SCAN
rs912767	SLC9A11	cis	parietal	SCAN
rs912767	RC3H1	cis	parietal	SCAN
rs912767	DARS2	cis	cerebellum	SCAN
rs912767	TNFSF4	cis	parietal	SCAN
rs912767	PRDX6	cis	cerebellum	SCAN
rs912767	DARS2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173448000-173477000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:173448600-173459800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr1:173448800-173458200	Strong transcription	Primary B cells from cord blood	blood
4	chr1:173448800-173459400	Weak transcription	Stomach Mucosa	stomach
5	chr1:173448800-173460000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:173449000-173458600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:173449000-173458800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:173449000-173458800	Strong transcription	Fetal Intestine Large	intestine
9	chr1:173449000-173459400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:173449000-173459400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:173449200-173456600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:173449200-173457000	Strong transcription	Fetal Kidney	kidney
13	chr1:173449200-173458800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:173449200-173459600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:173449400-173457800	Strong transcription	NHDF-Ad	bronchial
16	chr1:173449400-173458000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:173449400-173458600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:173449400-173458800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:173449400-173459200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:173449600-173457400	Strong transcription	NHEK	skin
21	chr1:173449600-173458000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:173449600-173458600	Strong transcription	Primary hematopoietic stem cells	blood
23	chr1:173449600-173458600	Strong transcription	HMEC	breast
24	chr1:173449600-173458600	Strong transcription	HUVEC	blood vessel
25	chr1:173449600-173458600	Strong transcription	NH-A	brain
26	chr1:173449600-173458600	Strong transcription	Osteobl	bone
27	chr1:173449600-173458800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:173449600-173458800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:173449600-173458800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:173449600-173458800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:173449600-173458800	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:173449600-173459200	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr1:173449600-173459400	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr1:173449600-173459400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:173449600-173459400	Strong transcription	HSMM	muscle
36	chr1:173449600-173459600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:173449600-173460000	Strong transcription	A549	lung
38	chr1:173449800-173457800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:173449800-173458400	Strong transcription	Hela-S3	cervix
40	chr1:173449800-173458600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:173449800-173458800	Strong transcription	Fetal Thymus	thymus
42	chr1:173449800-173459000	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:173449800-173459200	Strong transcription	Brain Hippocampus Middle	brain
44	chr1:173449800-173459400	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr1:173449800-173460000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:173450000-173458400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:173450000-173458400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:173450000-173458400	Strong transcription	NHLF	lung
49	chr1:173450000-173458600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:173450000-173458600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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