Variant report

Variant	rs12046751
Chromosome Location	chr1:74670172-74670173
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:74662984..74666783-chr1:74668983..74674031,7	K562	blood:

Variant related genes	Relation type
ENSG00000162620	Chromatin interaction
ENSG00000254685	Chromatin interaction
ENSG00000259030	Chromatin interaction
ENSG00000116783	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1032082	0.86[CHB][hapmap]
rs10493529	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs10789387	0.86[CHB][hapmap]
rs10789388	0.86[CHB][hapmap]
rs11210404	0.86[CHB][hapmap]
rs11210405	0.86[CHB][hapmap]
rs11210407	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap]
rs11210427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11210430	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11210433	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11210443	0.96[CEU][hapmap];0.80[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs12024616	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026140	0.92[CEU][hapmap];0.94[YRI][hapmap]
rs12029234	0.92[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs12029606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029814	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap]
rs12031026	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12033705	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap]
rs12036659	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs12038237	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12043976	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12048351	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs12122433	0.83[JPT][hapmap]
rs12402231	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12404294	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12410230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12410879	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746942	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs12746996	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs12747924	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483790	0.90[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1483795	0.86[CHB][hapmap]
rs17524893	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17526617	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17591640	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17591703	0.86[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs17592507	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1843023	0.86[CHB][hapmap]
rs1856789	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1930588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2035473	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs2128935	0.86[CHB][hapmap]
rs3765654	0.96[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs4142948	0.86[CHB][hapmap]
rs4596834	0.95[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs4650245	0.86[CHB][hapmap]
rs6676103	0.86[CHB][hapmap]
rs6676622	0.86[CHB][hapmap]
rs7529384	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs7535929	0.86[CHB][hapmap]
rs9804006	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]
rs9970514	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004451	chr1:74107125-74874389	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv534999	chr1:74107125-74874389	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv522147	chr1:74338530-74983835	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1013244	chr1:74441655-74680703	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	8 gene(s)	inside rSNPs	diseases
7	nsv535001	chr1:74441655-74680703	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv871269	chr1:74484753-74709362	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv871381	chr1:74484753-74712181	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv871084	chr1:74492200-74681968	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv871456	chr1:74492200-74712181	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv1008285	chr1:74517953-74705457	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv1011308	chr1:74545016-74932777	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv871630	chr1:74578318-74709362	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv871909	chr1:74594901-74703758	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
16	nsv428785	chr1:74640545-74818577	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
17	nsv870486	chr1:74654182-74804833	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12046751	LRRC44	Cis_1M	lymphoblastoid	RTeQTL
rs12046751	FPGT	cis	parietal	SCAN
rs12046751	TNNI3K	cis	parietal	SCAN
rs12046751	FPGT	cis	cerebellum	SCAN
rs12046751	RP11-439H8.4	cis	Muscle Skeletal	GTEx
rs12046751	TNNI3K	cis	cerebellum	SCAN
rs12046751	MGC22773	cis	multi-tissue	Pritchard
rs12046751	LRRIQ3	cis	Nerve Tibial	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:74664200-74672000	Weak transcription	Lung	lung
2	chr1:74664200-74672000	Weak transcription	Spleen	Spleen
3	chr1:74664200-74675200	Weak transcription	Pancreas	Pancrea
4	chr1:74664600-74671200	Weak transcription	Fetal Intestine Small	intestine
5	chr1:74664800-74670800	Weak transcription	Fetal Stomach	stomach
6	chr1:74664800-74672000	Weak transcription	Fetal Thymus	thymus
7	chr1:74664800-74673600	Weak transcription	NH-A	brain
8	chr1:74664800-74674000	Weak transcription	Fetal Kidney	kidney
9	chr1:74664800-74674600	Weak transcription	HSMMtube	muscle
10	chr1:74664800-74676000	Weak transcription	HSMM	muscle
11	chr1:74664800-74680400	Weak transcription	Fetal Brain Female	brain
12	chr1:74664800-74688200	Weak transcription	Psoas Muscle	Psoas
13	chr1:74665000-74670200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:74665000-74670200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:74665000-74670200	Weak transcription	NHLF	lung
16	chr1:74665000-74670400	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:74665000-74670400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:74665000-74671000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:74665000-74671000	Weak transcription	Brain Substantia Nigra	brain
20	chr1:74665000-74671600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:74665000-74672000	Weak transcription	HMEC	breast
22	chr1:74665000-74672200	Weak transcription	Colonic Mucosa	Colon
23	chr1:74665000-74672200	Weak transcription	HUVEC	blood vessel
24	chr1:74665000-74672600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:74665000-74673000	Weak transcription	Aorta	Aorta
26	chr1:74665000-74675000	Weak transcription	Osteobl	bone
27	chr1:74665000-74675600	Weak transcription	A549	lung
28	chr1:74665000-74677000	Weak transcription	Right Ventricle	heart
29	chr1:74665000-74690200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:74665200-74672600	Weak transcription	Brain Germinal Matrix	brain
31	chr1:74665400-74670200	Weak transcription	Ovary	ovary
32	chr1:74665400-74670800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:74665400-74672400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:74665400-74675000	Weak transcription	NHDF-Ad	bronchial
35	chr1:74665400-74675200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:74665400-74677200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:74665600-74670200	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:74665600-74670200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:74665600-74670200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:74665600-74670600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:74665600-74670600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:74665600-74671400	Strong transcription	Adipose Nuclei	Adipose
43	chr1:74665600-74671600	Weak transcription	Brain Angular Gyrus	brain
44	chr1:74665600-74671800	Weak transcription	Small Intestine	intestine
45	chr1:74665600-74671800	Weak transcription	GM12878-XiMat	blood
46	chr1:74665600-74672600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:74665600-74672600	Weak transcription	Dnd41	blood
48	chr1:74665600-74673400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:74665600-74674400	Weak transcription	Fetal Brain Male	brain
50	chr1:74665600-74677400	Weak transcription	Brain Anterior Caudate	brain

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