Variant report

Variant	rs300915
Chromosome Location	chr4:144274156-144274157
allele	C/T
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	GATA3	chr4:144273969-144274460	MCF-7	breast:	n/a	chr4:144274021-144274030 chr4:144274018-144274034 chr4:144274016-144274037
2	GATA1	chr4:144273837-144274319	PBDE	blood:	n/a	chr4:144274021-144274030 chr4:144274018-144274034 chr4:144274016-144274037
3	GATA3	chr4:144273789-144274516	SK-N-SH	brain:	n/a	chr4:144274021-144274030 chr4:144274018-144274034 chr4:144274016-144274037
4	JUND	chr4:144273870-144274254	K562	blood:	n/a	n/a
5	TAL1	chr4:144273857-144274177	K562	blood:	n/a	n/a
6	JUN	chr4:144273966-144274171	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:144268435..144271097-chr4:144272609..144275318,3	K562	blood:
2	chr4:144255276..144259485-chr4:144272162..144275884,5	MCF-7	breast:
3	chr4:144255601..144258477-chr4:144273085..144276456,3	MCF-7	breast:
4	chr4:144262793..144271335-chr4:144272377..144280163,14	K562	blood:
5	chr4:144105532..144107312-chr4:144271811..144274361,2	K562	blood:
6	chr4:144267296..144268822-chr4:144271997..144274488,2	MCF-7	breast:
7	chr4:144272183..144275049-chr4:144275578..144277182,2	MCF-7	breast:
8	chr4:144272912..144279199-chr4:144279482..144284125,11	K562	blood:

Variant related genes	Relation type
ENSG00000228981	TF binding region
ENSG00000178972	Chromatin interaction
ENSG00000170185	Chromatin interaction
ENSG00000109458	Chromatin interaction
ENSG00000265623	Chromatin interaction
ENSG00000228981	Chromatin interaction
ENSG00000250326	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10012713	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10013047	0.87[ASN][1000 genomes]
rs1027851	0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1027852	0.87[ASN][1000 genomes]
rs10519691	0.86[CHD][hapmap]
rs11100786	0.85[ASN][1000 genomes]
rs11100787	0.84[ASN][1000 genomes]
rs11100788	0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11730569	0.87[ASN][1000 genomes]
rs11945731	0.80[ASN][1000 genomes]
rs11947952	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12647531	0.87[ASN][1000 genomes]
rs12649592	0.85[ASN][1000 genomes]
rs13101346	0.87[ASN][1000 genomes]
rs13123498	0.89[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1397528	0.89[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap];0.86[LWK][hapmap];0.85[YRI][hapmap]
rs1472873	0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs1510879	0.80[ASN][1000 genomes]
rs1510880	0.89[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1866756	0.87[ASN][1000 genomes]
rs2013856	0.80[ASN][1000 genomes]
rs2048408	0.85[ASN][1000 genomes]
rs2055730	0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs2119270	0.85[ASN][1000 genomes]
rs2196908	0.87[ASN][1000 genomes]
rs2196909	0.87[ASN][1000 genomes]
rs300890	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs300891	0.80[ASN][1000 genomes]
rs300892	0.81[ASN][1000 genomes]
rs300893	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs300894	0.95[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs300895	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs300899	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs300901	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs300902	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs300903	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs300904	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs300905	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs300910	0.94[ASN][1000 genomes]
rs300911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs300912	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs300913	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];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300914	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][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]
rs300916	1.00[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs300917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs300918	0.94[ASN][1000 genomes]
rs300919	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs300943	0.95[CEU][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs300946	0.85[EUR][1000 genomes]
rs300947	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs300951	0.95[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs300953	0.87[EUR][1000 genomes]
rs34439737	0.83[ASN][1000 genomes]
rs3792652	0.89[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3792653	0.85[ASN][1000 genomes]
rs3792655	0.87[ASN][1000 genomes]
rs3805238	0.89[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs3805245	0.85[ASN][1000 genomes]
rs3805246	0.87[ASN][1000 genomes]
rs3805247	0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3805249	0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs3805251	0.88[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs3805252	0.85[ASN][1000 genomes]
rs3805253	0.89[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3805254	0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs3805256	0.89[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3805257	0.82[CEU][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs3828512	0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3828513	0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs3828514	0.85[ASN][1000 genomes]
rs55758499	0.87[ASN][1000 genomes]
rs55894236	0.87[ASN][1000 genomes]
rs568685	0.80[ASN][1000 genomes]
rs592349	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62337488	0.80[ASN][1000 genomes]
rs624170	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs624189	0.80[ASN][1000 genomes]
rs6537154	0.84[ASN][1000 genomes]
rs6537155	0.89[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs666542	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs713140	0.89[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs719392	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7680959	0.89[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs906571	0.87[ASN][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	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1026110	chr4:144239825-144292148	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs300915	SLC10A7	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144259600-144276200	Weak transcription	Fetal Kidney	kidney
2	chr4:144263000-144276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:144263000-144277800	Weak transcription	Fetal Thymus	thymus
4	chr4:144264000-144276400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:144265600-144276400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:144265800-144276400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:144269800-144276400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:144270000-144275000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:144270000-144275200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:144270000-144277600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:144270200-144275200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:144271400-144275600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr4:144272000-144274200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:144272000-144274800	Enhancers	Placenta Amnion	Placenta Amnion
15	chr4:144272000-144275000	Enhancers	Brain Angular Gyrus	brain
16	chr4:144272000-144279200	Enhancers	Brain Anterior Caudate	brain
17	chr4:144272000-144281400	Enhancers	Brain Substantia Nigra	brain
18	chr4:144272200-144274200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:144272200-144274200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr4:144272200-144274200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:144272200-144274400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr4:144272200-144274400	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr4:144272200-144274400	Enhancers	Brain Germinal Matrix	brain
24	chr4:144272400-144274200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr4:144272400-144274400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr4:144272400-144274400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:144272400-144275400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:144272400-144275400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr4:144272400-144276600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr4:144272400-144279200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:144272600-144274400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr4:144272600-144274400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:144272600-144274400	Enhancers	HUVEC	blood vessel
34	chr4:144272600-144274600	Flanking Active TSS	Fetal Heart	heart
35	chr4:144272600-144274600	Enhancers	HMEC	breast
36	chr4:144272600-144275000	Enhancers	Fetal Intestine Large	intestine
37	chr4:144272600-144275400	Enhancers	Liver	Liver
38	chr4:144272600-144275400	Enhancers	Duodenum Mucosa	Duodenum
39	chr4:144272600-144275400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr4:144272600-144275600	Enhancers	NHEK	skin
41	chr4:144272800-144274400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:144272800-144275600	Enhancers	Fetal Stomach	stomach
43	chr4:144272800-144276400	Weak transcription	Lung	lung
44	chr4:144272800-144280200	Enhancers	Colon Smooth Muscle	Colon
45	chr4:144272800-144281200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr4:144272800-144284600	Enhancers	Fetal Intestine Small	intestine
47	chr4:144272800-144299800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr4:144273000-144274200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr4:144273000-144274200	Enhancers	Colonic Mucosa	Colon
50	chr4:144273000-144274400	Flanking Active TSS	K562	blood

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