Variant report

Variant	rs29000286
Chromosome Location	chr8:103219495-103219496
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:103217322..103219597-chr8:103250656..103252706,2	K562	blood:
2	chr8:103219476..103221329-chr8:103222779..103224814,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246263	Chromatin interaction
ENSG00000048392	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10505019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1052069	1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs1052071	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs11774420	0.81[ASN][1000 genomes]
rs11774459	0.81[ASN][1000 genomes]
rs11776865	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11777942	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs11778107	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11783467	0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11784180	0.81[ASN][1000 genomes]
rs11784534	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11785514	0.94[ASN][1000 genomes]
rs11786397	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869269	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869276	0.81[ASN][1000 genomes]
rs16869282	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16869295	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs16918482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293984	1.00[CHB][hapmap]
rs2387995	0.81[ASN][1000 genomes]
rs28928571	0.81[ASN][1000 genomes]
rs28928592	0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28928597	0.81[ASN][1000 genomes]
rs28999671	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28999676	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28999706	0.81[ASN][1000 genomes]
rs29000274	0.81[ASN][1000 genomes]
rs29000294	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3735720	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3735721	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3735722	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3907099	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4329248	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5005121	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57901015	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57978361	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60604862	0.94[ASN][1000 genomes]
rs7836046	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs7841131	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv891242	chr8:103210971-103282418	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs29000286	NCALD	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103209600-103223000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:103209800-103219600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr8:103209800-103219600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr8:103209800-103221600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr8:103209800-103221600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr8:103209800-103222200	Weak transcription	Left Ventricle	heart
7	chr8:103209800-103223400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr8:103209800-103223600	Weak transcription	NH-A	brain
9	chr8:103209800-103224400	Weak transcription	Fetal Intestine Large	intestine
10	chr8:103209800-103224800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr8:103209800-103225400	Weak transcription	Fetal Kidney	kidney
12	chr8:103209800-103225600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr8:103209800-103229600	Weak transcription	A549	lung
14	chr8:103209800-103229800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr8:103209800-103229800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr8:103209800-103230400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr8:103209800-103230400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr8:103209800-103230400	Weak transcription	Aorta	Aorta
19	chr8:103209800-103230400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr8:103209800-103230400	Weak transcription	Thymus	Thymus
21	chr8:103209800-103230800	Weak transcription	Right Ventricle	heart
22	chr8:103209800-103233400	Weak transcription	Esophagus	oesophagus
23	chr8:103209800-103233800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr8:103209800-103236800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr8:103209800-103239200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr8:103209800-103244800	Weak transcription	Stomach Mucosa	stomach
27	chr8:103210000-103219800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr8:103210000-103223000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr8:103210000-103223000	Weak transcription	Placenta	Placenta
30	chr8:103210000-103223200	Weak transcription	Fetal Thymus	thymus
31	chr8:103210000-103229800	Weak transcription	Brain Hippocampus Middle	brain
32	chr8:103210000-103230200	Weak transcription	Brain Angular Gyrus	brain
33	chr8:103210200-103219600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr8:103210200-103224400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr8:103210400-103219600	Weak transcription	NHDF-Ad	bronchial
36	chr8:103210600-103222400	Weak transcription	Fetal Muscle Leg	muscle
37	chr8:103210600-103222800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr8:103210600-103223000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr8:103210600-103225000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr8:103210600-103239600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:103210800-103232000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr8:103211000-103230400	Weak transcription	Fetal Brain Female	brain
43	chr8:103213600-103223000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr8:103214600-103222800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr8:103215000-103229600	Weak transcription	HUVEC	blood vessel
46	chr8:103215600-103248400	Weak transcription	Psoas Muscle	Psoas
47	chr8:103216000-103227400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr8:103216200-103227400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr8:103216200-103229800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr8:103216200-103230400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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