Variant report

Variant	rs6478972
Chromosome Location	chr9:101869278-101869279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101869195..101872022-chr9:101900402..101902081,2	K562	blood:
2	chr9:101866361..101869341-chr9:101886452..101890095,3	MCF-7	breast:
3	chr9:101866534..101869508-chr9:101907295..101910821,3	MCF-7	breast:
4	chr9:101671905..101674026-chr9:101868875..101871020,2	K562	blood:

Variant related genes	Relation type
ENSG00000252942	Chromatin interaction
ENSG00000106799	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1013186	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs10283455	0.94[CEU][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs10733708	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10733709	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10739778	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs10739779	0.94[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs10760667	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10760668	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10760669	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10760670	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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760671	0.94[CEU][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10760672	0.94[CEU][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10760673	0.81[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10760674	0.82[ASN][1000 genomes]
rs10819634	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10819635	1.00[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10819636	0.84[ASN][1000 genomes]
rs10819637	0.89[EUR][1000 genomes]
rs10819638	0.94[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10819639	0.89[CEU][hapmap]
rs10819640	0.82[ASN][1000 genomes]
rs10988703	0.87[EUR][1000 genomes]
rs10988706	0.94[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10988709	0.84[ASN][1000 genomes]
rs10988713	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs10988714	0.89[EUR][1000 genomes]
rs10988715	0.84[ASN][1000 genomes]
rs10988716	0.94[CEU][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10988717	0.82[ASN][1000 genomes]
rs10988723	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11568752	0.84[ASN][1000 genomes]
rs12346650	1.00[ASW][hapmap];0.90[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12685571	0.84[ASN][1000 genomes]
rs12686783	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1571589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1571590	0.94[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs1590	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1626340	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1699413	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1888223	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1888225	0.83[ASN][1000 genomes]
rs1973518	0.82[ASN][1000 genomes]
rs2026811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334348	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs334349	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs334351	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs334353	0.87[ASW][hapmap];0.89[CEU][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs334354	0.81[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs334355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334356	0.94[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs334357	0.94[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs334358	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs334362	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs334363	0.83[ASN][1000 genomes]
rs334364	0.83[ASN][1000 genomes]
rs334365	0.92[ASN][1000 genomes]
rs334366	0.83[ASN][1000 genomes]
rs334367	0.83[ASN][1000 genomes]
rs334370	0.81[ASN][1000 genomes]
rs334371	0.91[ASN][1000 genomes]
rs367568	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3739798	0.83[ASN][1000 genomes]
rs383496	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs401186	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs420549	0.94[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs44466	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs597457	0.94[CEU][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6478973	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7022989	0.85[CHB][hapmap]
rs7031302	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031309	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042852	0.89[CEU][hapmap];0.90[CHD][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7043624	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7874221	0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs789675	0.80[EUR][1000 genomes]
rs868	0.94[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]

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	nsv893618	chr9:101800106-101886071	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv893619	chr9:101835165-101936231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6478972	TGFBR1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101866600-101869400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr9:101866800-101869600	Active TSS	Lung	lung
3	chr9:101867000-101869400	Active TSS	Rectal Smooth Muscle	rectum
4	chr9:101867000-101869600	Active TSS	Placenta	Placenta
5	chr9:101867000-101870000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:101867000-101870000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:101868000-101869800	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr9:101868000-101869800	Flanking Active TSS	Dnd41	blood
9	chr9:101868000-101870600	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr9:101868200-101870000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr9:101868200-101870200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr9:101868200-101870200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:101868200-101870200	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr9:101868200-101870600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr9:101868200-101871000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:101868200-101871200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr9:101868400-101869400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr9:101868400-101869600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:101868400-101869600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:101868400-101869600	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr9:101868400-101869600	Flanking Active TSS	NHEK	skin
22	chr9:101868400-101869800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:101868400-101869800	Flanking Active TSS	NHLF	lung
24	chr9:101868400-101870200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:101868400-101870400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:101868400-101870600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr9:101868400-101870800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr9:101868400-101871000	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr9:101868400-101871200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:101868400-101871800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:101868400-101872200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:101868400-101872600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr9:101868400-101881400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:101868400-101896400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:101868600-101869400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:101868600-101869400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:101868600-101869400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr9:101868600-101869400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr9:101868600-101869400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr9:101868600-101869400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:101868600-101869400	Enhancers	Stomach Mucosa	stomach
42	chr9:101868600-101869400	Flanking Active TSS	HSMMtube	muscle
43	chr9:101868600-101869600	Weak transcription	Brain Angular Gyrus	brain
44	chr9:101868600-101869600	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr9:101868600-101869800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:101868600-101869800	Active TSS	Brain Hippocampus Middle	brain
47	chr9:101868600-101869800	Flanking Active TSS	Fetal Brain Male	brain
48	chr9:101868600-101869800	Flanking Active TSS	NHDF-Ad	bronchial
49	chr9:101868600-101870000	Weak transcription	Small Intestine	intestine
50	chr9:101868600-101870000	Enhancers	HepG2	liver

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