Variant report

Variant	rs2374190
Chromosome Location	chr12:31535747-31535748
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM60A-3	chr12:31535160-31537109	NONHSAT027548
2	lnc-FAM60A-3	chr12:31535654-31536163	NONHSAT027549

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1012154	0.85[CHB][hapmap]
rs11051456	0.90[AMR][1000 genomes]
rs1150942	0.81[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs1150953	0.85[CHB][hapmap]
rs1150954	0.94[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs1150955	0.85[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs1259235	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs1259386	0.90[CHB][hapmap]
rs1259405	0.90[CEU][hapmap]
rs1259409	0.94[CEU][hapmap];0.92[CHB][hapmap]
rs1259437	0.90[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs1272773	0.90[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs1716216	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs2061761	0.90[CEU][hapmap]
rs2568884	0.85[CHB][hapmap]
rs2568887	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs2568902	0.83[ASN][1000 genomes]
rs2617191	0.81[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs2617200	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs2682695	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]
rs2682697	0.91[CHB][hapmap]
rs4482118	0.83[ASW][hapmap]
rs708200	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs708212	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs708215	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs708217	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7294574	0.88[ASW][hapmap]
rs792871	0.91[CHB][hapmap]
rs792875	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793148	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]
rs793150	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs793158	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs793161	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793171	0.81[CEU][hapmap]
rs793174	0.90[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs793176	0.84[CHB][hapmap]
rs793177	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs793186	0.90[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs793191	0.80[CEU][hapmap];0.92[CHB][hapmap]
rs7959877	0.83[ASW][hapmap]
rs7962896	0.83[ASW][hapmap]
rs7974437	0.88[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap]
rs7975761	0.88[ASW][hapmap]
rs7976644	0.83[ASW][hapmap]
rs899159	0.92[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS 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	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS 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	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2374190	DENND5B	cis	parietal	SCAN
rs2374190	PTHLH	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31523400-31537600	Weak transcription	Fetal Brain Female	brain
2	chr12:31523800-31538200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:31524400-31536600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr12:31524400-31538200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:31524400-31540200	Weak transcription	Brain Hippocampus Middle	brain
6	chr12:31524800-31537200	Weak transcription	Fetal Intestine Large	intestine
7	chr12:31524800-31538000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:31530800-31538000	Weak transcription	Liver	Liver
9	chr12:31530800-31541400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:31531800-31539600	Weak transcription	HSMM	muscle
11	chr12:31532800-31538800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:31533600-31537400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:31534000-31539000	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:31534200-31538000	Weak transcription	A549	lung
15	chr12:31534400-31540400	Weak transcription	Psoas Muscle	Psoas
16	chr12:31534600-31537200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:31534800-31538400	Weak transcription	Ovary	ovary
18	chr12:31534800-31538600	Weak transcription	Fetal Intestine Small	intestine
19	chr12:31534800-31541800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:31535000-31538000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr12:31535000-31538200	Weak transcription	Adipose Nuclei	Adipose
22	chr12:31535000-31538200	Weak transcription	Left Ventricle	heart
23	chr12:31535000-31539000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:31535200-31538000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:31535200-31538200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:31535200-31538200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr12:31535200-31538200	Weak transcription	Brain Anterior Caudate	brain
28	chr12:31535400-31538000	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr12:31535400-31538200	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr12:31535400-31538200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:31535400-31538200	Weak transcription	Aorta	Aorta
32	chr12:31535400-31538400	Weak transcription	Brain Germinal Matrix	brain
33	chr12:31535400-31538800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:31535400-31541800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:31535600-31536000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:31535600-31536400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:31535600-31537200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr12:31535600-31539000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr12:31535600-31560600	Weak transcription	Osteobl	bone

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