Variant report

Variant	rs13150320
Chromosome Location	chr4:174149111-174149112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:174141903..174144401-chr4:174146766..174149389,2	K562	blood:
2	chr4:174089332..174093564-chr4:174145332..174150414,5	MCF-7	breast:
3	chr4:174149045..174150839-chr4:174157691..174160667,3	K562	blood:
4	chr4:174123757..174125470-chr4:174148883..174150972,2	K562	blood:
5	chr4:174146730..174148234-chr4:174148547..174151368,2	K562	blood:

Variant related genes	Relation type
ENSG00000245213	Chromatin interaction
ENSG00000109586	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10005325	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10520255	0.85[CEU][hapmap];0.90[TSI][hapmap]
rs10520256	0.92[CEU][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11942280	0.85[CEU][hapmap];0.90[TSI][hapmap]
rs13116270	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13123399	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13124470	0.91[CEU][hapmap]
rs13141844	0.92[CEU][hapmap]
rs13150231	0.83[AMR][1000 genomes]
rs13151627	0.85[CEU][hapmap];0.90[TSI][hapmap]
rs17059205	0.91[CEU][hapmap]
rs17059207	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs17059217	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17059234	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17059235	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1991726	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2332658	0.92[CEU][hapmap]
rs28361970	0.80[EUR][1000 genomes]
rs28694391	0.92[EUR][1000 genomes]
rs34285915	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34971958	0.81[EUR][1000 genomes]
rs35576170	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35679682	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35730812	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35796775	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36050097	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4380500	0.87[EUR][1000 genomes]
rs4608791	0.92[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs4696054	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs62341096	0.82[EUR][1000 genomes]
rs62342296	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62342297	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6553686	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6822924	0.85[CEU][hapmap]
rs6835517	1.00[GIH][hapmap]
rs722826	0.85[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs722827	0.85[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs7667345	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7668473	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs7673747	0.80[EUR][1000 genomes]
rs7681286	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9685410	0.83[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs9995556	0.92[CEU][hapmap];0.93[TSI][hapmap]

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	esv1799519	chr4:174090004-174173743	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv3378663	chr4:174149108-174149646	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13150320	GALNT7	cis	cerebellum	SCAN
rs13150320	SCRG1	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174104000-174157200	Weak transcription	Ovary	ovary
2	chr4:174114200-174157800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:174114600-174155000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:174123600-174174200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:174126000-174156400	Weak transcription	Brain Anterior Caudate	brain
6	chr4:174126400-174149800	Weak transcription	Esophagus	oesophagus
7	chr4:174126600-174155200	Weak transcription	GM12878-XiMat	blood
8	chr4:174126600-174163400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:174127000-174163600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr4:174127000-174163600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:174128200-174169200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:174131800-174156400	Weak transcription	Fetal Intestine Small	intestine
13	chr4:174131800-174168600	Weak transcription	Gastric	stomach
14	chr4:174132800-174150600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr4:174136600-174158400	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:174136800-174157200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:174139000-174157600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:174140000-174150600	Weak transcription	Primary T cells from cord blood	blood
19	chr4:174140400-174158200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:174140400-174163400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:174140400-174163600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:174140400-174163600	Weak transcription	Aorta	Aorta
23	chr4:174140600-174149800	Weak transcription	Dnd41	blood
24	chr4:174140600-174150800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:174140600-174158000	Weak transcription	Hela-S3	cervix
26	chr4:174140600-174158200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:174140600-174158600	Weak transcription	HSMMtube	muscle
28	chr4:174142200-174173400	Weak transcription	Lung	lung
29	chr4:174143600-174155000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:174144200-174169000	Weak transcription	Fetal Intestine Large	intestine
31	chr4:174145200-174155000	Weak transcription	Primary B cells from cord blood	blood
32	chr4:174145800-174163800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:174145800-174163800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:174146400-174149200	Weak transcription	Spleen	Spleen
35	chr4:174146800-174150400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:174148000-174149200	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr4:174148000-174150000	Weak transcription	K562	blood
38	chr4:174148000-174150600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr4:174148000-174150800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:174148000-174151200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:174148000-174152400	Weak transcription	Thymus	Thymus
42	chr4:174148000-174153200	Weak transcription	Fetal Thymus	thymus
43	chr4:174148000-174154800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:174148000-174155200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr4:174148000-174155400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:174148000-174156400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr4:174148000-174157200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:174148000-174157400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr4:174148000-174173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:174148200-174154000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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