Variant report

Variant	rs2108981
Chromosome Location	chr17:19878666-19878667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19877195..19879459-chr17:19883535..19885344,2	K562	blood:
2	chr17:19858887..19861543-chr17:19877180..19878762,2	K562	blood:
3	chr17:19877498..19879131-chr17:19879770..19882757,2	MCF-7	breast:
4	chr17:19877816..19880542-chr17:20058157..20059665,2	MCF-7	breast:
5	chr17:19875702..19877605-chr17:19877615..19879225,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1009082	1.00[CHB][hapmap]
rs10438824	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12449662	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936794	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12943369	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12944084	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12946508	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12947950	1.00[CHB][hapmap]
rs12949485	1.00[CHB][hapmap]
rs1638526	0.86[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1638527	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1638528	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs169413	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604987	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17605101	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17668529	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17686622	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17686839	1.00[CHB][hapmap]
rs17759609	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs1812934	1.00[CHB][hapmap]
rs203449	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs203454	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs203464	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs203467	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs203474	0.89[EUR][1000 genomes]
rs203475	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203476	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs203478	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs203480	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2703794	1.00[CHB][hapmap]
rs34089239	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs34182788	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34726000	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35254155	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35315252	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35925051	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35979784	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36097967	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862151	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs427033	0.86[CEU][hapmap]
rs4577147	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4588033	1.00[CHB][hapmap]
rs4924802	1.00[CHB][hapmap]
rs4924809	1.00[CHB][hapmap]
rs4924810	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4925054	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4925063	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925064	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925075	0.87[MEX][hapmap]
rs4925084	1.00[CHB][hapmap]
rs56005410	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066345	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62066346	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066347	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066348	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066349	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066350	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066351	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066352	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62067482	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62067483	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6813	0.86[CEU][hapmap];0.93[GIH][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7209653	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8079923	0.91[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs850622	0.91[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9891503	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9901294	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2108981	SMCR5	cis	parietal	SCAN
rs2108981	AKAP10	cis	lymphoblastoid	seeQTL
rs2108981	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19840000-19879200	Weak transcription	Fetal Brain Male	brain
2	chr17:19850600-19879200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:19850600-19880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:19850600-19880200	Weak transcription	Aorta	Aorta
5	chr17:19852200-19879400	Weak transcription	Esophagus	oesophagus
6	chr17:19852200-19879600	Weak transcription	Right Ventricle	heart
7	chr17:19852200-19880000	Weak transcription	Psoas Muscle	Psoas
8	chr17:19857400-19880400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:19857600-19880200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr17:19859800-19879400	Weak transcription	Brain Angular Gyrus	brain
11	chr17:19861800-19880000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr17:19862000-19879000	Weak transcription	Brain Substantia Nigra	brain
13	chr17:19862000-19879200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr17:19862000-19880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr17:19862000-19880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr17:19862200-19880000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr17:19863400-19879600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr17:19863600-19879800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr17:19865000-19879600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr17:19865200-19880200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr17:19865800-19879000	Weak transcription	Brain Anterior Caudate	brain
22	chr17:19866200-19879000	Weak transcription	Brain Hippocampus Middle	brain
23	chr17:19866400-19879400	Weak transcription	Spleen	Spleen
24	chr17:19869000-19880200	Weak transcription	HSMMtube	muscle
25	chr17:19869200-19879400	Weak transcription	Stomach Mucosa	stomach
26	chr17:19870200-19880000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr17:19870400-19879000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr17:19872000-19880000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr17:19872000-19880200	Weak transcription	Colonic Mucosa	Colon
30	chr17:19872600-19879200	Weak transcription	Osteobl	bone
31	chr17:19872600-19879400	Weak transcription	Left Ventricle	heart
32	chr17:19872600-19879600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr17:19872600-19880000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr17:19872800-19879400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr17:19872800-19879600	Weak transcription	Lung	lung
36	chr17:19873000-19879200	Weak transcription	HMEC	breast
37	chr17:19873400-19879200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr17:19873600-19879000	Weak transcription	Fetal Kidney	kidney
39	chr17:19873600-19879200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr17:19873600-19879200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr17:19873600-19879400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr17:19873600-19879800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr17:19873600-19880000	Weak transcription	NHDF-Ad	bronchial
44	chr17:19873800-19879000	Strong transcription	A549	lung
45	chr17:19873800-19879200	Weak transcription	K562	blood
46	chr17:19874000-19879400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr17:19874000-19879400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr17:19874200-19880000	Weak transcription	Fetal Muscle Leg	muscle
49	chr17:19874400-19879400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr17:19874400-19880400	Weak transcription	Ovary	ovary

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