Variant report

Variant	rs12230757
Chromosome Location	chr12:4464458-4464459
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11063081	0.82[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11063105	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11063110	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11063112	0.88[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11063123	0.82[ASN][1000 genomes]
rs11063127	0.80[ASN][1000 genomes]
rs11063129	0.80[ASN][1000 genomes]
rs11063130	0.80[ASN][1000 genomes]
rs12231368	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12819556	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12819956	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12823289	0.88[CEU][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12823931	0.87[CHB][hapmap];1.00[LWK][hapmap]
rs13312789	0.82[ASW][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.88[ASN][1000 genomes]
rs16931344	0.80[ASN][1000 genomes]
rs17773299	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs3812822	0.87[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs6489538	0.80[ASN][1000 genomes]
rs7133330	0.86[ASW][hapmap];0.88[CEU][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7316649	0.87[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs7955866	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7961824	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7976548	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7978281	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv468985	chr12:4423612-4473329	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv557122	chr12:4423612-4473329	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv519278	chr12:4441906-4475194	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv528492	chr12:4462161-4473329	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv523578	chr12:4462505-4467921	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12230757	CLEC4A	cis	parietal	SCAN
rs12230757	LRRC23	cis	parietal	SCAN
rs12230757	NECAP1	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4431200-4465800	Weak transcription	Psoas Muscle	Psoas
2	chr12:4431600-4465000	Weak transcription	Pancreas	Pancrea
3	chr12:4434000-4465000	Weak transcription	Esophagus	oesophagus
4	chr12:4441000-4465600	Weak transcription	Fetal Intestine Large	intestine
5	chr12:4443400-4464800	Weak transcription	Fetal Brain Male	brain
6	chr12:4447400-4464800	Weak transcription	Right Ventricle	heart
7	chr12:4447600-4464800	Weak transcription	Brain Germinal Matrix	brain
8	chr12:4448000-4464800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:4449200-4465000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:4449400-4466000	Weak transcription	NHDF-Ad	bronchial
11	chr12:4450000-4465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:4455600-4465000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:4456000-4464800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:4456000-4464800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr12:4456000-4465200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:4456400-4464800	Weak transcription	Brain Angular Gyrus	brain
17	chr12:4458000-4464800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:4461200-4465000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:4461800-4465000	Weak transcription	Gastric	stomach
20	chr12:4461800-4467800	Weak transcription	NHEK	skin
21	chr12:4462000-4464600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:4462000-4464800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:4462000-4465800	Weak transcription	Hela-S3	cervix
24	chr12:4462000-4466400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:4462000-4467400	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:4462200-4464600	Weak transcription	Liver	Liver
27	chr12:4462200-4465000	Weak transcription	Left Ventricle	heart
28	chr12:4462200-4466800	Weak transcription	NHLF	lung
29	chr12:4462200-4467000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:4462200-4468000	Weak transcription	Fetal Brain Female	brain
31	chr12:4462400-4465400	Weak transcription	Osteobl	bone
32	chr12:4462400-4465800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:4462600-4464800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:4462600-4464800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr12:4462600-4467000	Weak transcription	HSMM	muscle
36	chr12:4462600-4468000	Weak transcription	Primary B cells from cord blood	blood
37	chr12:4462800-4464800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr12:4462800-4465000	Weak transcription	Adipose Nuclei	Adipose
39	chr12:4462800-4465000	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:4462800-4465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:4462800-4465000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:4462800-4465000	Weak transcription	NH-A	brain
43	chr12:4462800-4465400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr12:4462800-4465400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:4462800-4466000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr12:4462800-4466400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:4462800-4467800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:4462800-4467800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:4462800-4467800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:4462800-4468200	Weak transcription	GM12878-XiMat	blood

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