Variant report

Variant	rs829696
Chromosome Location	chr2:30651080-30651081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30453036..30455279-chr2:30649671..30652674,3	K562	blood:
2	chr2:30453451..30455867-chr2:30649615..30651171,2	K562	blood:
3	chr2:30643130..30645110-chr2:30649070..30651101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213626	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10167083	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10175399	0.85[JPT][hapmap]
rs10183928	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12053428	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12468064	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1252625	0.85[JPT][hapmap]
rs1252631	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1252646	0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs1252651	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252654	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1525062	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs1662946	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1869423	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs1869424	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap]
rs1975555	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs2121600	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2123753	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2177698	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2593442	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2602808	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs4952147	0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs6731031	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs6740440	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs7580496	0.88[AFR][1000 genomes]
rs7583211	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7591110	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7592355	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs829563	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829564	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829565	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829574	0.85[JPT][hapmap]
rs829575	0.85[JPT][hapmap];0.85[TSI][hapmap]
rs829581	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829582	0.85[JPT][hapmap]
rs829618	0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs829619	0.85[JPT][hapmap]
rs829620	0.85[JPT][hapmap]
rs829622	0.85[JPT][hapmap]
rs829630	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs829631	0.85[JPT][hapmap]
rs829632	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs829634	0.85[JPT][hapmap]
rs829639	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829641	0.81[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs829642	0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs829646	0.85[JPT][hapmap];0.81[TSI][hapmap]
rs829653	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs829654	0.85[JPT][hapmap]
rs829655	0.85[JPT][hapmap]
rs829659	0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs829661	0.85[JPT][hapmap]
rs829664	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap]
rs829669	0.85[JPT][hapmap]
rs829671	0.85[JPT][hapmap]
rs829672	0.85[JPT][hapmap]
rs829673	0.85[JPT][hapmap]
rs829675	0.85[JPT][hapmap]
rs829677	0.85[JPT][hapmap]
rs829679	0.85[JPT][hapmap]
rs829680	0.85[JPT][hapmap]
rs829681	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829682	0.84[JPT][hapmap]
rs829684	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829694	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829699	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs829700	0.97[ASN][1000 genomes]
rs829701	0.90[ASN][1000 genomes]
rs844194	0.85[JPT][hapmap]
rs860487	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs866680	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv1799950	chr2:30632520-30654319	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs829696	TMEM214	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30645000-30652400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr2:30645600-30656600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:30645800-30656600	Weak transcription	Fetal Lung	lung
4	chr2:30646000-30653400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:30646400-30651200	Weak transcription	K562	blood
6	chr2:30646400-30651600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:30646400-30652400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr2:30646400-30656400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:30646400-30662600	Weak transcription	Thymus	Thymus
10	chr2:30647600-30651400	Weak transcription	Dnd41	blood
11	chr2:30647800-30659800	Weak transcription	Left Ventricle	heart
12	chr2:30648600-30655400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:30648600-30655400	Weak transcription	NHDF-Ad	bronchial
14	chr2:30648600-30655400	Weak transcription	Osteobl	bone
15	chr2:30648600-30659600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:30649000-30651600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr2:30649000-30652200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:30650000-30651800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr2:30650400-30651400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr2:30650600-30652800	Enhancers	Primary T cells from cord blood	blood
21	chr2:30650800-30651600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:30650800-30651600	Enhancers	Fetal Intestine Large	intestine
23	chr2:30650800-30651600	Enhancers	Stomach Mucosa	stomach
24	chr2:30650800-30651800	Enhancers	Fetal Heart	heart
25	chr2:30650800-30652200	Enhancers	Fetal Thymus	thymus
26	chr2:30651000-30651200	Enhancers	Gastric	stomach
27	chr2:30651000-30651400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:30651000-30651400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr2:30651000-30651400	Enhancers	Placenta Amnion	Placenta Amnion
30	chr2:30651000-30651400	Enhancers	HepG2	liver
31	chr2:30651000-30651600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:30651000-30651600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:30651000-30652000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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