Variant report

Variant	rs2028494
Chromosome Location	chr3:100004117-100004118
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100001262..100005277-chr3:100005969..100008923,3	K562	blood:
2	chr3:100002355..100004216-chr3:100007322..100009320,2	MCF-7	breast:
3	chr3:99904186..99906809-chr3:100003420..100005148,2	K562	blood:
4	chr3:100001256..100004272-chr3:100005969..100008923,4	K562	blood:

Variant related genes	Relation type
ENSG00000235156	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1036770	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936157	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11915985	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1214369	0.84[EUR][1000 genomes]
rs1214372	0.89[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs1214373	0.89[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs12696084	0.84[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs13070392	0.89[CEU][hapmap]
rs1609481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029162	1.00[CHB][hapmap]
rs277636	0.88[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs277637	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs277652	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs277654	0.88[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs277655	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs35939236	0.80[ASN][1000 genomes]
rs3772698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3862050	0.83[ASN][1000 genomes]
rs4552390	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928118	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4928119	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928169	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62281675	0.86[EUR][1000 genomes]
rs6763594	0.86[EUR][1000 genomes]
rs6802765	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6804963	0.95[CHB][hapmap];0.88[CHD][hapmap]
rs6808175	0.85[EUR][1000 genomes]
rs7427443	0.85[EUR][1000 genomes]
rs7618677	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs7630257	0.86[EUR][1000 genomes]
rs7637157	0.89[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs7638503	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs931332	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs967608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9863738	0.89[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs9880795	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs9882337	0.85[EUR][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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2028494	ZPLD1	cis	parietal	SCAN
rs2028494	TBC1D23	cis	Muscle Skeletal	GTEx
rs2028494	ZNF546	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-100037200	Weak transcription	Spleen	Spleen
2	chr3:99980600-100053200	Weak transcription	Gastric	stomach
3	chr3:99981200-100004800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:99981200-100030800	Weak transcription	Fetal Heart	heart
5	chr3:99981400-100004400	Weak transcription	Lung	lung
6	chr3:99982400-100005400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:99983200-100010000	Weak transcription	Pancreas	Pancrea
8	chr3:99984200-100010000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:99984200-100011000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:99986600-100024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:99988800-100013800	Weak transcription	Fetal Brain Male	brain
12	chr3:99989000-100005800	Weak transcription	Thymus	Thymus
13	chr3:99989000-100007600	Weak transcription	HUVEC	blood vessel
14	chr3:99989000-100025000	Weak transcription	Fetal Brain Female	brain
15	chr3:99990400-100005000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:99990400-100006000	Weak transcription	HSMMtube	muscle
17	chr3:99990600-100010600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:99990600-100030600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:99990800-100021400	Weak transcription	Psoas Muscle	Psoas
20	chr3:99991000-100006000	Weak transcription	Right Ventricle	heart
21	chr3:99992400-100017600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:99994200-100014200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:99994400-100007800	Weak transcription	Aorta	Aorta
24	chr3:99994400-100040800	Weak transcription	Esophagus	oesophagus
25	chr3:99995400-100019000	Weak transcription	Colonic Mucosa	Colon
26	chr3:99995800-100006000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:99996000-100012400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:99996000-100052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:99996000-100053000	Weak transcription	Small Intestine	intestine
30	chr3:99996400-100004200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:99996400-100025600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:99996800-100004800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:99996800-100010400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:99996800-100016800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:99997000-100008400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:99997000-100008800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:99997200-100011000	Weak transcription	Brain Substantia Nigra	brain
38	chr3:99997200-100017800	Weak transcription	Brain Angular Gyrus	brain
39	chr3:99997600-100004200	Weak transcription	Dnd41	blood
40	chr3:99997600-100017000	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:99997800-100007000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:99997800-100031800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:99998000-100011800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:99998000-100013600	Weak transcription	Fetal Kidney	kidney
45	chr3:99998200-100004200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:99998200-100005200	Strong transcription	HepG2	liver
47	chr3:99998200-100009600	Strong transcription	Primary T cells from cord blood	blood
48	chr3:99998200-100013400	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:99998200-100016200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:99998400-100006400	Strong transcription	NHDF-Ad	bronchial

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