Variant report

Variant	rs3773921
Chromosome Location	chr3:100455139-100455140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100448313..100450197-chr3:100453971..100455531,2	K562	blood:
2	chr3:100451065..100453351-chr3:100454518..100456261,2	K562	blood:
3	chr3:100452064..100453616-chr3:100453627..100456036,2	MCF-7	breast:
4	chr3:100427505..100430398-chr3:100453653..100455509,2	K562	blood:

Variant related genes	Relation type
ENSG00000114354	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1048364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10936314	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10936315	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1145335	0.81[ASN][1000 genomes]
rs1165261	0.83[ASN][1000 genomes]
rs11716316	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13064241	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13073146	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13078643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1503838	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1503839	0.83[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap]
rs1520649	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1553455	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16842544	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16842845	0.89[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap]
rs1994085	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2055543	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2169553	0.93[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2293030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34542266	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35353873	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35727175	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35734168	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3773924	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3862285	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4616685	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4928055	0.89[EUR][1000 genomes]
rs4928075	0.82[EUR][1000 genomes]
rs4928080	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4928082	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4928083	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4928085	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs544500	0.83[JPT][hapmap]
rs547330	0.83[JPT][hapmap]
rs60918523	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62274019	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7371847	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7372546	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7611116	0.81[EUR][1000 genomes]
rs7622313	0.82[ASN][1000 genomes]
rs7629121	0.89[EUR][1000 genomes]
rs7629392	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7632461	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7642598	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7644830	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs900233	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9290147	0.83[ASN][1000 genomes]
rs931206	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971230	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]
rs9838809	0.80[EUR][1000 genomes]
rs989793	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751965	chr3:100299310-100462527	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	esv2751966	chr3:100299310-100468500	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2751967	chr3:100299329-100455139	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv2751968	chr3:100299329-100476713	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv432466	chr3:100299329-100476713	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS 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	17 gene(s)	inside rSNPs	diseases
6	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
7	nsv877220	chr3:100324442-100467018	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv591157	chr3:100335088-100455139	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	esv2751971	chr3:100342493-100468500	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv460787	chr3:100350745-100467018	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv591164	chr3:100350745-100467018	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	esv2751973	chr3:100354170-100476713	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	esv2751974	chr3:100354170-100476713	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3773921	TFG	Cis_1M	lymphoblastoid	RTeQTL
rs3773921	CBLB	cis	parietal	SCAN
rs3773921	TFG	cis	Muscle Skeletal	GTEx
rs3773921	TFG	cis	multi-tissue	Pritchard
rs3773921	IMPG2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100429800-100455200	Weak transcription	Brain Substantia Nigra	brain
2	chr3:100429800-100475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:100430400-100473000	Strong transcription	Fetal Thymus	thymus
4	chr3:100431200-100473000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:100432400-100474400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr3:100432800-100473600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:100433000-100472400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:100434400-100478200	Weak transcription	Spleen	Spleen
9	chr3:100435600-100455400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:100436000-100474400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:100436600-100471600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:100436800-100473000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:100437000-100461600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr3:100437400-100472600	Strong transcription	Dnd41	blood
15	chr3:100437600-100475000	Strong transcription	Placenta	Placenta
16	chr3:100437800-100474400	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:100438800-100473800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:100441000-100456200	Weak transcription	Gastric	stomach
19	chr3:100441000-100458600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:100441000-100470800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:100441000-100473000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:100441000-100474400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:100441000-100479400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:100443200-100462200	Strong transcription	Adipose Nuclei	Adipose
25	chr3:100443400-100472200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:100443600-100466000	Strong transcription	Fetal Intestine Large	intestine
27	chr3:100444600-100471800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr3:100444600-100474400	Strong transcription	HSMM	muscle
29	chr3:100445200-100456200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:100445200-100457400	Strong transcription	Hela-S3	cervix
31	chr3:100445200-100470400	Strong transcription	HepG2	liver
32	chr3:100445400-100455400	Weak transcription	Right Atrium	heart
33	chr3:100445400-100472200	Weak transcription	Psoas Muscle	Psoas
34	chr3:100445400-100473800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:100445400-100475600	Weak transcription	Pancreas	Pancrea
36	chr3:100445600-100455200	Weak transcription	Brain Germinal Matrix	brain
37	chr3:100445600-100455400	Weak transcription	Brain Anterior Caudate	brain
38	chr3:100445800-100456000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:100445800-100459000	Weak transcription	Fetal Brain Male	brain
40	chr3:100446000-100455400	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:100446000-100470800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:100446200-100456600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:100447000-100456000	Weak transcription	Fetal Stomach	stomach
44	chr3:100447200-100471400	Strong transcription	HMEC	breast
45	chr3:100447400-100460000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:100447400-100473600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr3:100447600-100457600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:100447600-100461800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:100447600-100474200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:100447600-100477200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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