Variant report

Variant	rs1996664
Chromosome Location	chr3:49878395-49878396
allele	A/G
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	RAD21	chr3:49877757-49879312	SK-N-SH	brain:	n/a	chr3:49878753-49878772 chr3:49878756-49878769 chr3:49878646-49878658
2	CTCF	chr3:49878218-49879098	A549	lung:	n/a	chr3:49878544-49878552 chr3:49878645-49878655 chr3:49878229-49878238 chr3:49878545-49878553
3	CTCF	chr3:49878260-49878410	NHDF-neo	bronchial:	n/a	n/a
4	CTCF	chr3:49878160-49878410	HRE	kidney:	n/a	chr3:49878229-49878238
5	CTCF	chr3:49878280-49878430	GM12870	blood:	n/a	n/a
6	CTCF	chr3:49877838-49879078	SK-N-SH	brain:	n/a	chr3:49878544-49878552 chr3:49878645-49878655 chr3:49878229-49878238 chr3:49878545-49878553
7	CTCF	chr3:49878300-49878450	AG09309	skin:	n/a	n/a
8	CTCF	chr3:49878324-49879136	HCT-116	colon:	n/a	chr3:49878544-49878552 chr3:49878645-49878655 chr3:49878545-49878553

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49876541..49879414-chr3:49940769..49943993,4	K562	blood:

Variant related genes	Relation type
TRAIP	TF binding region
ENSG00000228008	Chromatin interaction
ENSG00000164078	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10452032	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs1078341	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs11130217	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11709734	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11720705	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12715437	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13071931	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs1491985	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1799844	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1996663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329021	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs28535523	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs35129566	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4855845	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs4855846	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs4855882	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4855885	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs55997059	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58339610	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59357103	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59684465	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61557789	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260663	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62260720	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62260723	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262722	0.94[EUR][1000 genomes]
rs62262730	0.95[EUR][1000 genomes]
rs6774202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs6790568	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6804970	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6809879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7613603	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7615318	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs7620848	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7621797	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7628207	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7635601	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs7637711	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7649428	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9829155	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9835157	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9836756	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9849038	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9851651	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9870755	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9870858	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1996664	GMPPB	cis	parietal	SCAN
rs1996664	AMT	cis	lymphoblastoid	seeQTL
rs1996664	DALRD3	cis	cerebellum	SCAN
rs1996664	P4HTM	cis	parietal	SCAN
rs1996664	OR9G4	trans	parietal	SCAN
rs1996664	AMT	cis	Thyroid	GTEx
rs1996664	AMT	cis	lung	GTEx
rs1996664	AMT	cis	parietal	SCAN
rs1996664	RNF123	cis	parietal	SCAN
rs1996664	DALRD3	cis	parietal	SCAN
rs1996664	QRICH1	cis	cerebellum	SCAN
rs1996664	GNL3	cis	cerebellum	SCAN
rs1996664	ZNF589	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49861200-49882200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:49861200-49893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:49863400-49879000	Weak transcription	Fetal Brain Male	brain
4	chr3:49863800-49879000	Weak transcription	NH-A	brain
5	chr3:49863800-49882800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:49864000-49883200	Weak transcription	Colonic Mucosa	Colon
7	chr3:49864000-49893200	Weak transcription	Placenta	Placenta
8	chr3:49864200-49893000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:49864600-49882000	Weak transcription	Osteobl	bone
10	chr3:49864800-49880400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:49864800-49886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:49865000-49886000	Strong transcription	Dnd41	blood
13	chr3:49865600-49885800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:49865600-49885800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:49866000-49881000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:49867800-49879000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:49868200-49878600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:49869000-49883200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:49869200-49879000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr3:49869200-49881000	Weak transcription	HMEC	breast
21	chr3:49869400-49878400	Weak transcription	K562	blood
22	chr3:49869400-49879600	Weak transcription	Primary T cells from cord blood	blood
23	chr3:49869400-49880400	Weak transcription	Spleen	Spleen
24	chr3:49869400-49893000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:49869600-49880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:49869800-49878400	Weak transcription	Fetal Intestine Large	intestine
27	chr3:49869800-49879400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:49869800-49879600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:49870000-49878600	Weak transcription	HepG2	liver
30	chr3:49870200-49893000	Weak transcription	HSMM	muscle
31	chr3:49870600-49878800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:49871200-49886000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:49873600-49885800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:49873800-49878600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:49873800-49885800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:49874000-49885800	Strong transcription	Thymus	Thymus
37	chr3:49874800-49879400	Strong transcription	GM12878-XiMat	blood
38	chr3:49874800-49882000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:49876000-49878400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:49876000-49879400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:49876000-49879400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:49876000-49880600	Weak transcription	NHEK	skin
43	chr3:49876000-49880800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:49876000-49881800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:49876000-49882800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:49876200-49880600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:49876400-49878400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:49876400-49878800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:49876400-49879200	Enhancers	Fetal Muscle Trunk	muscle
50	chr3:49876600-49878800	Enhancers	Fetal Muscle Leg	muscle

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