Variant report

Variant	rs9978131
Chromosome Location	chr21:46212580-46212581
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46208115..46211415-chr21:46211594..46214545,4	MCF-7	breast:
2	chr21:46188637..46191346-chr21:46209977..46212870,2	MCF-7	breast:
3	chr21:46202815..46206353-chr21:46211210..46215151,6	K562	blood:
4	chr21:45557514..45558447-chr21:46212556..46213412,2	K562	blood:
5	chr21:46212466..46215146-chr21:46219897..46223000,3	MCF-7	breast:
6	chr21:46207093..46209545-chr21:46210264..46213746,3	K562	blood:
7	chr21:46211611..46213164-chr21:46493063..46494889,2	K562	blood:
8	chr21:46211786..46214681-chr21:46493090..46494686,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000235374	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13047692	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13047718	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13051119	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13433413	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17004706	0.86[MEX][hapmap]
rs2294158	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2838676	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2838677	0.81[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2838679	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838681	0.89[YRI][hapmap]
rs2838683	0.91[YRI][hapmap]
rs2838693	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838697	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838698	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838700	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34875321	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788138	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4818731	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4818976	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818977	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72613649	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8131444	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8132011	0.83[AMR][1000 genomes]
rs9306115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9306116	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9637189	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9808690	0.86[MEX][hapmap]
rs9977465	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9977676	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9981344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs9984290	0.81[LWK][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9978131	ITGB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46187000-46213000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr21:46189000-46221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr21:46193400-46212600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr21:46193800-46212800	Weak transcription	Psoas Muscle	Psoas
5	chr21:46195000-46212600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr21:46195000-46219800	Weak transcription	Small Intestine	intestine
7	chr21:46195400-46220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr21:46197200-46213000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr21:46197200-46220400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr21:46197400-46212800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr21:46198800-46213000	Weak transcription	Brain Angular Gyrus	brain
12	chr21:46198800-46219600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr21:46198800-46220000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr21:46198800-46220000	Weak transcription	Fetal Kidney	kidney
15	chr21:46200000-46220400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr21:46200400-46212800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr21:46200400-46218200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr21:46200600-46212800	Weak transcription	Colon Smooth Muscle	Colon
19	chr21:46201200-46220400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:46201600-46212600	Weak transcription	Gastric	stomach
21	chr21:46201600-46212800	Weak transcription	Right Atrium	heart
22	chr21:46201600-46212800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr21:46202400-46219200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr21:46203400-46220000	Weak transcription	Fetal Brain Female	brain
25	chr21:46204000-46212600	Weak transcription	Ovary	ovary
26	chr21:46205200-46213000	Weak transcription	Brain Substantia Nigra	brain
27	chr21:46205200-46213000	Weak transcription	Left Ventricle	heart
28	chr21:46205200-46213200	Weak transcription	Esophagus	oesophagus
29	chr21:46205200-46220400	Weak transcription	Aorta	Aorta
30	chr21:46205200-46220800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr21:46205400-46212800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr21:46205600-46212600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr21:46205800-46212800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr21:46206200-46212600	Weak transcription	Fetal Heart	heart
35	chr21:46206200-46212600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr21:46206200-46213000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr21:46206200-46216200	Weak transcription	Placenta	Placenta
38	chr21:46206200-46218400	Weak transcription	Brain Anterior Caudate	brain
39	chr21:46206200-46219800	Weak transcription	Right Ventricle	heart
40	chr21:46206200-46220000	Weak transcription	Brain Germinal Matrix	brain
41	chr21:46206400-46212600	Weak transcription	Pancreas	Pancrea
42	chr21:46206400-46212800	Weak transcription	HMEC	breast
43	chr21:46206400-46220000	Weak transcription	Brain Hippocampus Middle	brain
44	chr21:46206600-46212600	Weak transcription	Fetal Lung	lung
45	chr21:46206800-46213000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr21:46206800-46220000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr21:46207800-46212600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr21:46207800-46212800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr21:46209400-46212600	Strong transcription	K562	blood
50	chr21:46209400-46212600	Strong transcription	NHEK	skin

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