Variant report

Variant	rs10496663
Chromosome Location	chr2:128228898-128228899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:128228866-128229213	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:128220774..128223723-chr2:128228116..128231015,2	K562	blood:
2	chr2:128223739..128227371-chr2:128227403..128230155,4	K562	blood:
3	chr2:128219868..128222726-chr2:128227473..128229280,2	MCF-7	breast:
4	chr2:128223739..128227156-chr2:128228484..128231083,5	K562	blood:

Variant related genes	Relation type
RNU4-48P	TF binding region
ENSG00000231731	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10928769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11679431	1.00[ASW][hapmap];0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs11681225	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11682864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11685630	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11688201	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11690086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11892245	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs12053309	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233101	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12616200	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12618494	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12619972	0.84[EUR][1000 genomes]
rs12620037	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12623334	0.85[EUR][1000 genomes]
rs13011041	0.85[EUR][1000 genomes]
rs13389029	0.86[EUR][1000 genomes]
rs17015274	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17015334	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1864553	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2082182	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap]
rs2099209	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2288655	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732205	0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889307	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56100618	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56106399	0.86[EUR][1000 genomes]
rs56261855	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56327685	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58880408	0.86[EUR][1000 genomes]
rs62156572	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62156576	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62160289	0.84[EUR][1000 genomes]
rs62160291	0.85[EUR][1000 genomes]
rs6716489	0.86[EUR][1000 genomes]
rs6758364	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7586672	0.87[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.87[LWK][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs777556	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs873099	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	esv3693423	chr2:128223875-128230794	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10496663	AC068282.3	cis	Esophagus Mucosa	GTEx
rs10496663	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs10496663	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs10496663	AC068282.3	cis	Whole Blood	GTEx
rs10496663	AC068282.3	cis	Muscle Skeletal	GTEx
rs10496663	AC068282.3	cis	lung	GTEx
rs10496663	AC068282.3	cis	Esophagus Muscularis	GTEx
rs10496663	AC068282.3	cis	Artery Tibial	GTEx
rs10496663	AC068282.3	cis	Nerve Tibial	GTEx
rs10496663	AC068282.3	cis	Thyroid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128206200-128237800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:128206800-128233600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:128208400-128238800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:128209000-128238000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:128209200-128237600	Weak transcription	Adipose Nuclei	Adipose
6	chr2:128210000-128237600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:128210200-128238000	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:128211600-128237600	Weak transcription	Right Ventricle	heart
9	chr2:128213000-128237600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:128213200-128237800	Weak transcription	Colonic Mucosa	Colon
11	chr2:128213400-128237800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:128213600-128237600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:128213600-128237800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:128213800-128238000	Weak transcription	Brain Germinal Matrix	brain
15	chr2:128216200-128233600	Weak transcription	GM12878-XiMat	blood
16	chr2:128219800-128237600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:128220400-128239800	Weak transcription	Fetal Lung	lung
18	chr2:128221600-128229000	Weak transcription	HepG2	liver
19	chr2:128221600-128230200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:128221600-128237400	Weak transcription	HSMM	muscle
21	chr2:128221600-128237600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:128222200-128237800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:128222400-128237600	Weak transcription	Osteobl	bone
24	chr2:128222400-128237800	Weak transcription	Fetal Brain Female	brain
25	chr2:128222600-128237000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:128222600-128237200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:128222800-128230400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:128222800-128233400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:128222800-128237600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:128222800-128237800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:128222800-128239600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:128223000-128237600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:128223200-128237000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:128223200-128237000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:128223200-128237600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr2:128223200-128237600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:128223200-128237800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:128223200-128237800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:128223400-128237000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:128223600-128268800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:128223800-128238400	Weak transcription	K562	blood
42	chr2:128224000-128241800	Weak transcription	Small Intestine	intestine
43	chr2:128224600-128237800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:128224800-128237600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:128225800-128233400	Weak transcription	HUVEC	blood vessel
46	chr2:128226200-128244000	Weak transcription	Psoas Muscle	Psoas
47	chr2:128227400-128233000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:128227400-128233000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr2:128227400-128237800	Weak transcription	Primary B cells from cord blood	blood
50	chr2:128227400-128237800	Weak transcription	A549	lung

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