Variant report

Variant	rs10520255
Chromosome Location	chr4:174114089-174114090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:174111282..174114186-chr4:174114823..174117851,4	K562	blood:
2	chr4:174113250..174114451-chr4:174178602..174179153,3	MCF-7	breast:
3	chr4:174103126..174105789-chr4:174112551..174114903,2	MCF-7	breast:
4	chr4:174087959..174091632-chr4:174112021..174114740,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245213	Chromatin interaction
ENSG00000109586	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10005325	0.87[EUR][1000 genomes]
rs10471199	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10520256	0.92[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs11722807	0.91[JPT][hapmap]
rs11731262	0.83[JPT][hapmap]
rs11734517	0.83[JPT][hapmap]
rs11942280	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13102038	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13116270	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs13117810	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13120215	0.94[EUR][1000 genomes]
rs13123359	0.90[EUR][1000 genomes]
rs13123399	0.85[CEU][hapmap]
rs13124470	0.92[CEU][hapmap]
rs13141844	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs13142524	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13150231	0.80[EUR][1000 genomes]
rs13150320	0.85[CEU][hapmap];0.90[TSI][hapmap]
rs13151627	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481120	0.82[JPT][hapmap]
rs17059153	0.86[CHB][hapmap]
rs17059154	0.84[CHB][hapmap]
rs17059205	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs17059207	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs17059217	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17059235	0.85[CEU][hapmap]
rs1991726	0.85[CEU][hapmap]
rs2332657	0.95[EUR][1000 genomes]
rs2332658	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs28361970	0.90[EUR][1000 genomes]
rs28413646	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34285915	0.82[EUR][1000 genomes]
rs34718403	0.94[EUR][1000 genomes]
rs35576170	0.88[EUR][1000 genomes]
rs35644315	0.85[EUR][1000 genomes]
rs35679682	0.81[EUR][1000 genomes]
rs35730812	0.84[EUR][1000 genomes]
rs36050097	0.88[EUR][1000 genomes]
rs3775590	0.83[JPT][hapmap]
rs3775591	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4380500	0.84[EUR][1000 genomes]
rs4608791	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs4695827	0.90[EUR][1000 genomes]
rs4695829	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4696050	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696054	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs61241252	0.80[ASN][1000 genomes]
rs62341096	0.83[EUR][1000 genomes]
rs6553686	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs6822924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835517	0.81[CEU][hapmap]
rs6842693	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6858043	0.90[EUR][1000 genomes]
rs722826	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs722827	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs7661977	0.94[EUR][1000 genomes]
rs7664847	0.83[JPT][hapmap]
rs7665469	0.92[JPT][hapmap]
rs7667345	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs7668435	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7668473	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs7669267	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs7672055	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs7673747	0.90[EUR][1000 genomes]
rs7686909	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs7689781	0.81[CEU][hapmap]
rs934358	0.85[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs9685410	0.85[CEU][hapmap];0.90[TSI][hapmap]
rs9991863	0.95[EUR][1000 genomes]
rs9995556	0.92[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10520255	GALNT7	cis	cerebellum	SCAN
rs10520255	SCRG1	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174104000-174157200	Weak transcription	Ovary	ovary
2	chr4:174105000-174116400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:174106600-174114200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:174107000-174117800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:174107400-174120800	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:174107600-174115400	Weak transcription	Primary B cells from cord blood	blood
7	chr4:174107600-174115400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr4:174107800-174116200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:174108600-174114200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:174108800-174126800	Weak transcription	Spleen	Spleen
11	chr4:174109000-174116600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr4:174110200-174116400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:174110200-174118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:174110600-174117000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr4:174111000-174116800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr4:174111200-174114600	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr4:174111200-174116800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:174111400-174114200	Enhancers	Fetal Intestine Small	intestine
19	chr4:174111800-174114200	Enhancers	H9 Cell Line	embryonic stem cell
20	chr4:174111800-174114200	Enhancers	Dnd41	blood
21	chr4:174111800-174114200	Enhancers	HMEC	breast
22	chr4:174112000-174114200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr4:174112000-174114200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr4:174112000-174114200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr4:174112000-174114400	Enhancers	Fetal Thymus	thymus
26	chr4:174112200-174114400	Enhancers	Stomach Mucosa	stomach
27	chr4:174112400-174114200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:174112400-174114200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:174112400-174114400	Enhancers	Primary T cells from cord blood	blood
30	chr4:174112600-174114200	Enhancers	HSMM	muscle
31	chr4:174112600-174114400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:174112600-174131200	Weak transcription	Colonic Mucosa	Colon
33	chr4:174112800-174114600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr4:174112800-174115200	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr4:174112800-174122800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:174112800-174126200	Weak transcription	Pancreas	Pancrea
37	chr4:174112800-174126400	Weak transcription	Gastric	stomach
38	chr4:174112800-174127000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:174112800-174140000	Weak transcription	Aorta	Aorta
40	chr4:174113000-174114200	Enhancers	Hela-S3	cervix
41	chr4:174113000-174116400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr4:174113000-174116400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:174113000-174120400	Weak transcription	HSMMtube	muscle
44	chr4:174113200-174114200	Enhancers	Primary hematopoietic stem cells	blood
45	chr4:174113200-174116200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:174113200-174116400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:174113400-174114200	Enhancers	A549	lung
48	chr4:174113400-174114400	Enhancers	Thymus	Thymus
49	chr4:174113400-174116400	Weak transcription	Brain Angular Gyrus	brain
50	chr4:174113400-174117400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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