Variant report

Variant	rs7634963
Chromosome Location	chr3:46737979-46737980
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	MAX	chr3:46737714-46738063	K562	blood:	n/a	chr3:46737714-46737730
2	MYC	chr3:46737748-46738085	MCF10A-Er-Src	breast:	n/a	n/a
3	MXI1	chr3:46737475-46738207	IMR90	lung:	n/a	n/a
4	CTCF	chr3:46737920-46738070	SAEC	small airway:	n/a	chr3:46737998-46738011
5	MYC	chr3:46737682-46738066	MCF10A-Er-Src	breast:	n/a	chr3:46737714-46737730
6	MAX	chr3:46736886-46738056	NB4	blood:	n/a	chr3:46737182-46737191 chr3:46737714-46737730
7	FOS	chr3:46737844-46738038	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr3:46737893-46737996	K562	blood:	n/a	n/a
9	MAX	chr3:46737754-46738019	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:46734988..46739707-chr3:46741491..46746249,8	K562	blood:
2	chr3:46732167..46733968-chr3:46737534..46740232,2	MCF-7	breast:
3	chr3:46733050..46735013-chr3:46736523..46739104,3	K562	blood:
4	chr3:46736085..46739130-chr3:47020544..47022434,3	MCF-7	breast:
5	chr3:46736001..46738313-chr3:46739420..46741660,3	MCF-7	breast:
6	chr3:46737124..46738860-chr3:46743430..46745835,2	K562	blood:
7	chr3:46736421..46738516-chr3:46947579..46949832,2	MCF-7	breast:

Variant related genes	Relation type
ALS2CL	TF binding region
TMIE	TF binding region
ENSG00000160796	Chromatin interaction
ENSG00000160799	Chromatin interaction
ENSG00000181585	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11711074	0.83[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12496585	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3210183	0.83[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs34190208	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3935248	0.83[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4076927	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4682825	0.82[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs55650397	0.81[ASN][1000 genomes]
rs55991232	0.84[EUR][1000 genomes]
rs56069285	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56313683	0.82[ASN][1000 genomes]
rs56670151	0.95[ASN][1000 genomes]
rs59191033	0.83[ASN][1000 genomes]
rs61277784	0.81[EUR][1000 genomes]
rs62246183	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6442020	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6776464	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6792255	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6804514	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7372799	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7373358	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73831197	0.83[ASN][1000 genomes]
rs7426833	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7610936	0.90[ASN][1000 genomes]
rs7613489	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7615747	0.83[AMR][1000 genomes]
rs7625303	0.81[EUR][1000 genomes]
rs7633016	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7642448	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7642783	0.83[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7649081	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7650366	0.83[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv516623	chr3:46680063-46852679	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv1804680	chr3:46704348-46869911	Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv876742	chr3:46705369-46763839	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	nsv536555	chr3:46706571-46817963	Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv536556	chr3:46706571-46849443	Genic enhancers Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv536557	chr3:46706571-46853434	Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
15	esv1797503	chr3:46708712-46760713	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
16	nsv876743	chr3:46716523-46753577	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
17	nsv876744	chr3:46716523-46763839	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
18	nsv460525	chr3:46728659-46790397	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
19	nsv590179	chr3:46728659-46790397	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
20	esv1847964	chr3:46729757-46753976	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7634963	ALS2CL	cis	Muscle Skeletal	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46735000-46739000	Enhancers	Spleen	Spleen
2	chr3:46735400-46738000	Enhancers	Dnd41	blood
3	chr3:46735400-46738000	Weak transcription	NH-A	brain
4	chr3:46735400-46739000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr3:46735600-46738000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:46735600-46738000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr3:46735600-46738000	Enhancers	Primary hematopoietic stem cells	blood
8	chr3:46735600-46738000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:46735600-46738000	Enhancers	Pancreas	Pancrea
10	chr3:46735600-46738000	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr3:46735600-46738200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:46735600-46738400	Enhancers	Thymus	Thymus
13	chr3:46735600-46738400	Enhancers	HUVEC	blood vessel
14	chr3:46735600-46738600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr3:46735600-46738600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:46735600-46738600	Enhancers	Fetal Thymus	thymus
17	chr3:46735600-46739000	Enhancers	Liver	Liver
18	chr3:46735600-46739000	Enhancers	Right Atrium	heart
19	chr3:46735600-46739200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr3:46735600-46739200	Enhancers	Left Ventricle	heart
21	chr3:46735600-46739200	Enhancers	Lung	lung
22	chr3:46735600-46739400	Enhancers	Psoas Muscle	Psoas
23	chr3:46735600-46742600	Weak transcription	Aorta	Aorta
24	chr3:46735800-46738000	Enhancers	Primary B cells from peripheral blood	blood
25	chr3:46735800-46738000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:46735800-46738000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:46735800-46738200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:46735800-46738200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:46735800-46738200	Enhancers	HMEC	breast
30	chr3:46735800-46738400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:46735800-46738400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:46735800-46738400	Enhancers	Brain Angular Gyrus	brain
33	chr3:46735800-46738400	Enhancers	Esophagus	oesophagus
34	chr3:46735800-46738600	Enhancers	Colonic Mucosa	Colon
35	chr3:46735800-46738600	Enhancers	Duodenum Mucosa	Duodenum
36	chr3:46735800-46738800	Enhancers	Placenta	Placenta
37	chr3:46735800-46739000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr3:46735800-46739000	Enhancers	Primary T cells fromperipheralblood	blood
39	chr3:46735800-46739200	Enhancers	Fetal Muscle Leg	muscle
40	chr3:46735800-46739400	Enhancers	Right Ventricle	heart
41	chr3:46735800-46742000	Weak transcription	Fetal Brain Male	brain
42	chr3:46736000-46738200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:46736000-46738800	Enhancers	Fetal Stomach	stomach
44	chr3:46736200-46739000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr3:46736200-46739200	Enhancers	Colon Smooth Muscle	Colon
46	chr3:46736200-46739400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr3:46736600-46738200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr3:46736600-46738600	Enhancers	Gastric	stomach
49	chr3:46736800-46738000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr3:46736800-46738000	Enhancers	Placenta Amnion	Placenta Amnion

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