Variant report

Variant	rs971230
Chromosome Location	chr3:100478315-100478316
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100476994..100479281-chr3:100486300..100488381,2	K562	blood:
2	chr3:100473925..100475796-chr3:100476025..100478809,2	MCF-7	breast:
3	chr3:100477781..100481491-chr3:100485242..100489259,3	K562	blood:
4	chr3:100468860..100470969-chr3:100476440..100479062,2	K562	blood:
5	chr3:100477399..100478933-chr3:100482930..100484757,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154175	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1048364	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10936314	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10936315	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11716316	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13064241	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13073146	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13078643	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13086822	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1503838	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1520649	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1553455	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16842544	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16842845	0.87[CEU][hapmap]
rs1847391	0.81[EUR][1000 genomes]
rs1994085	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2055543	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2169553	0.91[CEU][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2293030	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34542266	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35353873	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35727175	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35734168	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3773921	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3773924	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3862285	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4616685	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4928055	0.84[EUR][1000 genomes]
rs4928080	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4928082	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4928083	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4928085	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4928086	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs544500	0.83[JPT][hapmap]
rs60918523	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62274019	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7371847	0.82[EUR][1000 genomes]
rs7372546	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7629121	0.83[EUR][1000 genomes]
rs7632461	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7642598	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7644830	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs900233	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs931206	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs989793	0.81[JPT][hapmap]

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	esv2751969	chr3:100312499-100479384	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv2751972	chr3:100342493-100493062	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv432469	chr3:100342493-100493062	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs971230	TFG	Cis_1M	lymphoblastoid	RTeQTL
rs971230	TFG	cis	Muscle Skeletal	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100441000-100479400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
3	chr3:100453200-100479000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:100457200-100480200	Weak transcription	Brain Angular Gyrus	brain
5	chr3:100467400-100497600	Weak transcription	Fetal Intestine Small	intestine
6	chr3:100468200-100488600	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:100469400-100480200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:100469600-100479200	Weak transcription	Fetal Brain Male	brain
9	chr3:100469800-100498200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:100469800-100501400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:100470200-100498400	Weak transcription	Right Ventricle	heart
12	chr3:100471000-100495800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:100471200-100480200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:100471600-100478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:100471600-100500400	Weak transcription	Lung	lung
16	chr3:100471800-100479400	Weak transcription	Fetal Kidney	kidney
17	chr3:100471800-100486200	Weak transcription	Brain Substantia Nigra	brain
18	chr3:100471800-100494600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:100471800-100502000	Weak transcription	Brain Anterior Caudate	brain
20	chr3:100472600-100484600	Weak transcription	NHEK	skin
21	chr3:100472800-100482800	Weak transcription	NHLF	lung
22	chr3:100472800-100494400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:100473000-100479800	Weak transcription	GM12878-XiMat	blood
24	chr3:100473000-100480400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:100473400-100480200	Weak transcription	A549	lung
26	chr3:100473400-100488400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:100473600-100480000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:100473600-100488600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:100473600-100488800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:100473600-100489200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:100473800-100484600	Weak transcription	HMEC	breast
32	chr3:100473800-100496400	Weak transcription	Fetal Intestine Large	intestine
33	chr3:100474000-100488800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:100474200-100482400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:100474400-100478800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:100474400-100480600	Weak transcription	Primary T cells from cord blood	blood
37	chr3:100474400-100484800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:100474400-100494200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:100474400-100500200	Weak transcription	HSMM	muscle
40	chr3:100474400-100501200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:100474800-100482800	Weak transcription	HSMMtube	muscle
42	chr3:100475000-100488000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:100475000-100499000	Weak transcription	Placenta	Placenta
44	chr3:100475600-100485600	Weak transcription	Left Ventricle	heart
45	chr3:100475600-100487600	Weak transcription	NHDF-Ad	bronchial
46	chr3:100475600-100520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:100475800-100478600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:100475800-100479400	Weak transcription	Adipose Nuclei	Adipose
49	chr3:100476400-100478400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:100477200-100480400	Weak transcription	H1 Cell Line	embryonic stem cell

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