Variant report

Variant	rs610578
Chromosome Location	chr12:121194565-121194566
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	chr12:121191123..121193615-chr12:121194473..121197241,2	K562	blood:
2	chr12:121161679..121164638-chr12:121193767..121195391,2	K562	blood:

Variant related genes	Relation type
ENSG00000122971	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10774567	0.95[ASN][1000 genomes]
rs1105416	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11065286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1151851	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap]
rs1168945	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1168954	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1168956	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1696363	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap]
rs1718211	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2454729	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2649996	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2649998	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2650006	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4767938	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs482522	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484456	0.95[ASN][1000 genomes]
rs487310	1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs487912	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs488172	0.95[ASN][1000 genomes]
rs493811	0.81[AMR][1000 genomes]
rs497273	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs516649	0.86[ASN][1000 genomes]
rs516978	0.97[ASN][1000 genomes]
rs532140	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs532703	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs550349	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs551087	0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs551125	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs558275	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs566704	0.97[ASN][1000 genomes]
rs566994	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs568297	0.97[ASN][1000 genomes]
rs584001	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs586305	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs589699	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs594507	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs619679	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs620772	0.86[ASN][1000 genomes]
rs623857	0.97[ASN][1000 genomes]
rs633084	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs634850	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6489779	0.95[ASN][1000 genomes]
rs6553	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs662284	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs662739	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs674021	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs679833	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs683091	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs683437	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs688402	0.80[CHB][hapmap];0.87[CHD][hapmap]
rs694303	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs697859	0.98[ASN][1000 genomes]
rs708785	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs790675	0.90[ASN][1000 genomes]
rs791210	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1041153	chr12:121171986-121208826	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs610578	WSB2	cis	cerebellum	SCAN
rs610578	SPPL3	cis	parietal	SCAN
rs610578	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs610578	SPPL3	cis	cerebellum	SCAN
rs610578	P2RX4	cis	cerebellum	SCAN
rs610578	PRKAB1	cis	parietal	SCAN
rs610578	UNC119B	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121168600-121196400	Weak transcription	Fetal Brain Female	brain
2	chr12:121177800-121197800	Weak transcription	Gastric	stomach
3	chr12:121179800-121197400	Weak transcription	Spleen	Spleen
4	chr12:121180200-121197400	Weak transcription	Pancreas	Pancrea
5	chr12:121183200-121197600	Weak transcription	Esophagus	oesophagus
6	chr12:121186400-121198400	Weak transcription	Right Ventricle	heart
7	chr12:121189600-121197000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:121190400-121197800	Weak transcription	Right Atrium	heart
9	chr12:121193000-121195600	Weak transcription	Fetal Stomach	stomach
10	chr12:121193000-121198400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:121193400-121195600	Weak transcription	Brain Germinal Matrix	brain
12	chr12:121193400-121197400	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:121193600-121197000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:121193800-121197600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:121193800-121198200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:121194000-121196800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:121194000-121197000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:121194000-121197600	Weak transcription	GM12878-XiMat	blood
19	chr12:121194000-121200800	Weak transcription	HepG2	liver
20	chr12:121194200-121195600	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:121194200-121197200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:121194200-121197600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:121194200-121197600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:121194200-121197800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:121194200-121197800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:121194200-121202200	Weak transcription	K562	blood
27	chr12:121194400-121194600	Enhancers	Placenta	Placenta
28	chr12:121194400-121195200	Enhancers	Fetal Intestine Small	intestine
29	chr12:121194400-121195800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr12:121194400-121196800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:121194400-121197000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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