Variant report

Variant	rs1538622
Chromosome Location	chr1:180512764-180512765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr1:180512557-180512866	HL-60	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180511395..180514188-chr1:180783985..180786756,2	K562	blood:
2	chr1:180512434..180513990-chr1:180599840..180601494,2	MCF-7	breast:
3	chr1:180511669..180514906-chr1:180530245..180533112,3	K562	blood:
4	chr1:180507839..180510458-chr1:180510629..180513153,2	K562	blood:
5	chr1:180511015..180513302-chr1:180517883..180519397,2	K562	blood:
6	chr1:180505841..180513650-chr1:180514886..180521271,14	K562	blood:
7	chr1:180505455..180510458-chr1:180510629..180513153,4	K562	blood:
8	chr1:180470537..180472654-chr1:180512131..180513964,2	MCF-7	breast:
9	chr1:180510781..180513155-chr1:180847874..180850004,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000266683	TF binding region
ENSG00000135847	Chromatin interaction
ENSG00000143324	Chromatin interaction
ENSG00000266683	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10494527	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap]
rs10753209	1.00[CEU][hapmap]
rs10753211	1.00[CEU][hapmap]
rs10753216	0.84[EUR][1000 genomes]
rs10798759	1.00[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap]
rs10798762	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap]
rs10798769	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs10798771	0.80[EUR][1000 genomes]
rs10798774	0.90[ASN][1000 genomes]
rs10798775	0.93[EUR][1000 genomes]
rs10913980	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap]
rs10913981	1.00[CEU][hapmap]
rs10913984	0.84[CEU][hapmap]
rs10913985	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap]
rs10913987	1.00[CEU][hapmap]
rs10914005	1.00[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap]
rs10914014	0.80[EUR][1000 genomes]
rs10914016	0.81[EUR][1000 genomes]
rs10914017	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs10914018	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10914023	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10914028	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10914034	0.88[ASN][1000 genomes]
rs10914036	0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs10914037	0.86[ASN][1000 genomes]
rs11580793	1.00[CEU][hapmap]
rs11799870	1.00[CEU][hapmap]
rs12024201	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes]
rs12034217	1.00[CEU][hapmap]
rs12039331	0.84[CHB][hapmap]
rs12069581	0.90[ASN][1000 genomes]
rs12136111	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12141348	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap]
rs12141848	1.00[CEU][hapmap]
rs12565492	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs12730889	1.00[CEU][hapmap]
rs1416821	1.00[CEU][hapmap]
rs1934410	0.93[EUR][1000 genomes]
rs2105232	0.80[EUR][1000 genomes]
rs4076403	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap]
rs4421553	1.00[CEU][hapmap]
rs4442335	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap]
rs4578179	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap]
rs4651068	0.88[ASN][1000 genomes]
rs4652505	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap]
rs6425644	0.81[CHB][hapmap]
rs6670544	1.00[CEU][hapmap]
rs6680202	0.88[ASN][1000 genomes]
rs6692401	0.88[ASN][1000 genomes]
rs6694798	0.84[ASN][1000 genomes]
rs6694975	0.88[ASN][1000 genomes]
rs6695171	0.86[ASN][1000 genomes]
rs6695263	0.88[ASN][1000 genomes]
rs6697924	1.00[CEU][hapmap]
rs6699076	0.86[CHB][hapmap]
rs6703124	0.88[ASN][1000 genomes]
rs72720947	0.86[ASN][1000 genomes]
rs7513944	0.90[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7513963	0.88[ASN][1000 genomes]
rs7515243	0.86[ASN][1000 genomes]
rs7517902	0.90[ASN][1000 genomes]
rs7528650	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs7532806	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs7540276	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes]
rs7541993	0.85[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs7543366	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes]
rs7546119	0.85[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs7550897	0.88[ASN][1000 genomes]
rs7551178	0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs7552084	0.85[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs946631	0.90[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.88[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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1538622	ACBD6	cis	parietal	SCAN
rs1538622	RNASEL	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180506200-180513200	Weak transcription	Pancreas	Pancrea
2	chr1:180507000-180514800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:180508000-180513200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:180508800-180513000	Enhancers	Fetal Heart	heart
5	chr1:180509400-180512800	Enhancers	Osteobl	bone
6	chr1:180509400-180513400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:180510200-180516000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:180510400-180513000	Enhancers	Fetal Brain Male	brain
9	chr1:180510400-180529400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:180511000-180513400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:180511200-180512800	Enhancers	Colon Smooth Muscle	Colon
12	chr1:180511200-180512800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr1:180511200-180513400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:180511200-180513400	Enhancers	Brain Anterior Caudate	brain
15	chr1:180511400-180512800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:180511600-180513200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:180511600-180516200	Weak transcription	Psoas Muscle	Psoas
18	chr1:180511800-180521200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:180512000-180512800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:180512000-180515800	Weak transcription	Left Ventricle	heart
21	chr1:180512200-180512800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:180512200-180513200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:180512200-180513200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:180512200-180513200	Weak transcription	Ovary	ovary
25	chr1:180512200-180513200	Weak transcription	Right Ventricle	heart
26	chr1:180512200-180513400	Weak transcription	Aorta	Aorta
27	chr1:180512200-180516200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:180512200-180516600	Weak transcription	Fetal Brain Female	brain
29	chr1:180512200-180521200	Weak transcription	HSMMtube	muscle
30	chr1:180512400-180515800	Weak transcription	Right Atrium	heart
31	chr1:180512400-180517800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:180512600-180516200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:180512600-180516200	Weak transcription	Brain Germinal Matrix	brain

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