Variant report

Variant	rs12039741
Chromosome Location	chr1:176135785-176135786
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	chr1:176130858..176132751-chr1:176134916..176136520,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10494495	0.80[CEU][hapmap]
rs10494498	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs10798434	0.80[CEU][hapmap]
rs10798442	0.80[CEU][hapmap]
rs10798446	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs10798447	0.81[EUR][1000 genomes]
rs10913128	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10913133	0.81[EUR][1000 genomes]
rs10913134	0.81[EUR][1000 genomes]
rs10913135	0.81[EUR][1000 genomes]
rs10913142	0.84[EUR][1000 genomes]
rs10913143	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs10913144	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs10913145	0.84[EUR][1000 genomes]
rs10913147	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs10913148	0.82[EUR][1000 genomes]
rs10913160	0.81[AMR][1000 genomes]
rs12033847	0.82[CEU][hapmap]
rs12033997	0.84[EUR][1000 genomes]
rs12034255	0.84[EUR][1000 genomes]
rs12040241	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12042918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12049077	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs12404596	0.82[CEU][hapmap]
rs12409108	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12724558	0.86[ASN][1000 genomes]
rs12755507	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17354120	0.82[EUR][1000 genomes]
rs2861672	0.84[EUR][1000 genomes]
rs34215167	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34511428	0.83[EUR][1000 genomes]
rs3748618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4526571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6673760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6678628	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs6678812	0.80[EUR][1000 genomes]
rs6684140	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7514517	0.83[EUR][1000 genomes]
rs7517503	0.82[EUR][1000 genomes]
rs7522843	0.80[EUR][1000 genomes]
rs7553759	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv548246	chr1:176043797-176136273	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv8558	chr1:176135063-176141916	Enhancers Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12039741	RP11-318C24.2	cis	Whole Blood	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176055000-176141600	Weak transcription	Hela-S3	cervix
2	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
3	chr1:176069000-176139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:176069200-176138800	Weak transcription	HUVEC	blood vessel
5	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
6	chr1:176072000-176140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:176085400-176142400	Weak transcription	Lung	lung
8	chr1:176096000-176138800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:176100800-176153200	Weak transcription	Colonic Mucosa	Colon
10	chr1:176110600-176164000	Weak transcription	NHLF	lung
11	chr1:176111800-176139400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:176116000-176146200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:176122000-176139800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:176123800-176139800	Weak transcription	Fetal Kidney	kidney
15	chr1:176123800-176144200	Weak transcription	Left Ventricle	heart
16	chr1:176123800-176150000	Weak transcription	Osteobl	bone
17	chr1:176126400-176168800	Weak transcription	Small Intestine	intestine
18	chr1:176126800-176139800	Weak transcription	HSMMtube	muscle
19	chr1:176127000-176147000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:176127000-176174000	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:176127200-176137800	Weak transcription	HSMM	muscle
22	chr1:176127200-176153400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:176127400-176139200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:176127400-176139600	Weak transcription	Brain Anterior Caudate	brain
25	chr1:176127400-176140200	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:176127400-176141200	Weak transcription	HMEC	breast
27	chr1:176127400-176143200	Weak transcription	Brain Substantia Nigra	brain
28	chr1:176127400-176144200	Weak transcription	A549	lung
29	chr1:176127400-176153400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:176127400-176155400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:176127600-176138200	Weak transcription	Fetal Brain Male	brain
32	chr1:176127600-176138800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:176127600-176139200	Weak transcription	Fetal Brain Female	brain
34	chr1:176128000-176139600	Weak transcription	Psoas Muscle	Psoas
35	chr1:176128000-176144200	Weak transcription	Gastric	stomach
36	chr1:176128000-176147000	Weak transcription	Stomach Mucosa	stomach
37	chr1:176128000-176157800	Weak transcription	Spleen	Spleen
38	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
39	chr1:176128200-176135800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:176128200-176136000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:176128200-176136200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:176128200-176138800	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:176128200-176139600	Weak transcription	Fetal Intestine Small	intestine
44	chr1:176128400-176154600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:176128600-176138800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:176128600-176147000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr1:176128600-176147200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:176128600-176155600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:176128800-176152800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:176128800-176152800	Weak transcription	Placenta Amnion	Placenta Amnion

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