Variant report

Variant	rs10242019
Chromosome Location	chr7:101527827-101527828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:101524538..101530208-chr7:101583819..101590225,13	MCF-7	breast:
2	chr7:101526287..101527935-chr7:101528596..101530450,2	K562	blood:
3	chr7:101527665..101530418-chr7:101615760..101617815,3	MCF-7	breast:
4	chr7:101500051..101501733-chr7:101526046..101528456,2	K562	blood:
5	chr7:101514608..101516122-chr7:101525582..101528029,2	K562	blood:
6	chr7:101486111..101487639-chr7:101525637..101527848,2	K562	blood:
7	chr7:101526289..101528067-chr7:101530737..101533297,2	K562	blood:
8	chr7:101457345..101464020-chr7:101524379..101528846,10	MCF-7	breast:
9	chr7:101512554..101516171-chr7:101524650..101528130,5	MCF-7	breast:
10	chr7:101526144..101529822-chr7:101529905..101534800,8	MCF-7	breast:
11	chr7:101456951..101464631-chr7:101524079..101528885,15	MCF-7	breast:
12	chr7:101526412..101529161-chr7:101615489..101617394,2	MCF-7	breast:
13	chr7:101524980..101528234-chr7:101584443..101587218,5	MCF-7	breast:
14	chr7:101524654..101529313-chr7:101536956..101539660,5	MCF-7	breast:
15	chr7:101525862..101528715-chr7:101557017..101559763,2	MCF-7	breast:
16	chr7:101527495..101530331-chr7:101553334..101556908,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10081174	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10226289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10227516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10240601	0.93[EUR][1000 genomes]
rs10241905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10255356	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10256232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10259103	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10259964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10261524	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10264844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10264855	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10264866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10271171	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10271610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10271838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10275899	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10279763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532535	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12534641	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12539310	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs13227531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13229243	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13236072	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13241079	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13241252	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2410921	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28409703	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34750675	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35065711	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4729756	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4729757	0.89[AMR][1000 genomes]
rs4729759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4729760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55824493	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60656667	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72603509	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs72603510	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72603511	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72603512	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9656073	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10242019	ZKSCAN5	cis	parietal	SCAN
rs10242019	MLL5	cis	cerebellum	SCAN
rs10242019	RINT1	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101521200-101528800	Enhancers	Fetal Heart	heart
2	chr7:101523200-101543200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:101523600-101528000	Enhancers	Duodenum Mucosa	Duodenum
4	chr7:101523600-101528600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:101523600-101529400	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr7:101523600-101529600	Enhancers	Rectal Smooth Muscle	rectum
7	chr7:101524800-101528200	Weak transcription	Right Ventricle	heart
8	chr7:101525400-101528000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr7:101526000-101528800	Enhancers	Dnd41	blood
10	chr7:101526000-101530200	Enhancers	Fetal Thymus	thymus
11	chr7:101526000-101540400	Weak transcription	Aorta	Aorta
12	chr7:101526200-101528200	Weak transcription	Lung	lung
13	chr7:101526200-101528400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:101526200-101528400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:101526200-101528400	Weak transcription	Ovary	ovary
16	chr7:101526200-101528400	Weak transcription	Pancreas	Pancrea
17	chr7:101526200-101528600	Weak transcription	Psoas Muscle	Psoas
18	chr7:101526200-101528600	Weak transcription	Spleen	Spleen
19	chr7:101526200-101528800	Enhancers	Colon Smooth Muscle	Colon
20	chr7:101526200-101528800	Enhancers	Hela-S3	cervix
21	chr7:101526200-101531400	Weak transcription	Esophagus	oesophagus
22	chr7:101526200-101536800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:101526400-101528000	Weak transcription	Primary B cells from cord blood	blood
24	chr7:101526400-101528200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:101526400-101528800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:101526400-101528800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr7:101526400-101529800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:101526400-101530000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr7:101526400-101533200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:101526400-101534600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:101526400-101542200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr7:101526600-101528000	Weak transcription	Brain Anterior Caudate	brain
33	chr7:101526600-101528000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr7:101526600-101528200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr7:101526600-101528200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:101526600-101528400	Weak transcription	Brain Substantia Nigra	brain
37	chr7:101526600-101529600	Enhancers	Liver	Liver
38	chr7:101526600-101533200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr7:101526800-101528000	Enhancers	K562	blood
40	chr7:101526800-101528200	Weak transcription	Brain Hippocampus Middle	brain
41	chr7:101526800-101528200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr7:101526800-101528200	Weak transcription	NHLF	lung
43	chr7:101526800-101528400	Weak transcription	Fetal Intestine Small	intestine
44	chr7:101526800-101528400	Weak transcription	Small Intestine	intestine
45	chr7:101526800-101528600	Enhancers	HepG2	liver
46	chr7:101526800-101529000	Weak transcription	Adipose Nuclei	Adipose
47	chr7:101526800-101529400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:101526800-101530200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr7:101526800-101531400	Enhancers	Left Ventricle	heart
50	chr7:101526800-101534600	Weak transcription	HSMMtube	muscle

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