Variant report

Variant	rs1929848
Chromosome Location	chr6:35200350-35200351
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35178562..35181407-chr6:35198838..35201388,2	MCF-7	breast:
2	chr6:35195991..35200691-chr6:35207151..35212650,5	K562	blood:
3	chr6:35182919..35187135-chr6:35197439..35201271,4	K562	blood:
4	chr6:35196232..35199243-chr6:35200230..35204307,5	K562	blood:
5	chr6:35191178..35195234-chr6:35198102..35200512,4	K562	blood:

Variant related genes	Relation type
ENSG00000272374	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1013907	0.81[EUR][1000 genomes]
rs11552398	1.00[GIH][hapmap]
rs1194	0.81[CEU][hapmap];0.80[MKK][hapmap];0.86[YRI][hapmap]
rs13216424	0.88[GIH][hapmap]
rs16871749	1.00[GIH][hapmap]
rs16871814	1.00[GIH][hapmap]
rs1888823	0.81[CEU][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs1929846	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929847	0.82[ASW][hapmap];0.81[CEU][hapmap];0.86[MKK][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs1929849	0.82[ASW][hapmap];0.81[CEU][hapmap];0.86[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2234044	1.00[GIH][hapmap]
rs2267658	0.81[EUR][1000 genomes]
rs2267662	0.81[CEU][hapmap];0.80[MKK][hapmap];0.86[YRI][hapmap]
rs2395617	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756856	1.00[GIH][hapmap]
rs3800392	0.81[CEU][hapmap];0.90[YRI][hapmap]
rs4711409	0.81[EUR][1000 genomes]
rs4713842	0.82[MEX][hapmap]
rs4713843	0.82[MEX][hapmap]
rs4713844	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457815	1.00[CHB][hapmap]
rs6902523	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs6906666	1.00[GIH][hapmap]
rs6919534	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920747	0.81[EUR][1000 genomes]
rs6928769	0.80[AFR][1000 genomes]
rs6931442	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707969	1.00[MEX][hapmap]
rs72909061	0.80[AFR][1000 genomes]
rs729925	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734538	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763155	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763157	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751726	1.00[CHB][hapmap]
rs7767150	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770619	1.00[CHB][hapmap]
rs820062	0.88[GIH][hapmap]
rs820065	0.88[GIH][hapmap]
rs820069	0.88[GIH][hapmap]
rs820095	1.00[GIH][hapmap]
rs820099	0.88[GIH][hapmap]
rs820101	0.88[GIH][hapmap]
rs9296144	0.80[CEU][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs9380501	0.81[CEU][hapmap];0.85[YRI][hapmap]
rs9394282	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462081	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9658077	1.00[CHB][hapmap]
rs9658081	1.00[CHB][hapmap]
rs9658085	1.00[CHB][hapmap]
rs9658089	1.00[CHD][hapmap]
rs9658118	1.00[CHD][hapmap]
rs9658119	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9658136	1.00[CHD][hapmap]
rs9658151	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs975496	0.81[CEU][hapmap];0.86[YRI][hapmap];0.81[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	esv3428128	chr6:35150524-35225843	Bivalent Enhancer Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1929848	TPM2	trans	lymphoblastoid	seeQTL
rs1929848	TULP1	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35182400-35209000	Weak transcription	A549	lung
2	chr6:35184800-35205600	Weak transcription	Fetal Brain Female	brain
3	chr6:35186200-35202800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:35186400-35212000	Weak transcription	NHDF-Ad	bronchial
5	chr6:35186600-35204600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:35186600-35205400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:35186800-35212000	Weak transcription	Dnd41	blood
8	chr6:35188200-35200400	Genic enhancers	Osteobl	bone
9	chr6:35188200-35205800	Weak transcription	Fetal Kidney	kidney
10	chr6:35188200-35206400	Weak transcription	NH-A	brain
11	chr6:35189600-35205800	Weak transcription	Brain Germinal Matrix	brain
12	chr6:35190000-35205600	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:35190200-35212000	Weak transcription	Brain Angular Gyrus	brain
14	chr6:35190600-35201800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:35191200-35212000	Weak transcription	Primary T cells from cord blood	blood
16	chr6:35191400-35226000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:35192200-35211400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:35194000-35201400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:35194000-35209400	Weak transcription	Thymus	Thymus
20	chr6:35194000-35225600	Weak transcription	Primary B cells from cord blood	blood
21	chr6:35194200-35202600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:35194800-35202800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:35195600-35210600	Weak transcription	Spleen	Spleen
24	chr6:35195800-35202400	Weak transcription	Fetal Intestine Small	intestine
25	chr6:35197000-35205600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:35197200-35201000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:35197400-35201400	Enhancers	Fetal Heart	heart
28	chr6:35197600-35200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:35198400-35202000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:35199200-35202600	Weak transcription	HSMMtube	muscle
31	chr6:35199200-35211800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:35199200-35212200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr6:35199400-35201000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:35199400-35201400	Weak transcription	Fetal Lung	lung
35	chr6:35199400-35201600	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr6:35199400-35208800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:35199400-35209200	Weak transcription	Adipose Nuclei	Adipose
38	chr6:35199400-35211800	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:35199400-35212000	Weak transcription	Brain Anterior Caudate	brain
40	chr6:35199400-35216200	Weak transcription	Brain Substantia Nigra	brain
41	chr6:35199600-35200400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:35199600-35201000	Weak transcription	Right Ventricle	heart
43	chr6:35199600-35202400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:35199600-35203000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:35199600-35203000	Strong transcription	Fetal Stomach	stomach
46	chr6:35199600-35204000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:35199600-35205400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:35199600-35209800	Weak transcription	Gastric	stomach
49	chr6:35199600-35210400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:35199600-35211200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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