Variant report

Variant	rs210643
Chromosome Location	chr6:117901283-117901284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:117890550..117892092-chr6:117899428..117901964,2	K562	blood:
2	chr6:117901081..117902881-chr6:117915482..117917190,2	K562	blood:
3	chr6:117893704..117895776-chr6:117900374..117902914,2	K562	blood:
4	chr6:117803317..117805281-chr6:117899805..117901348,2	MCF-7	breast:
5	chr6:117893704..117896609-chr6:117901239..117902914,2	K562	blood:
6	chr6:117901081..117903623-chr6:117915436..117916982,2	K562	blood:

Variant related genes	Relation type
ENSG00000164465	Chromatin interaction
ENSG00000047932	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11153678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153686	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11153687	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11153689	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12665677	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1472591	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17079404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs210616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210618	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs210621	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs210625	0.81[ASN][1000 genomes]
rs210627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs210628	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs210629	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs210631	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs210632	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs210634	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs210636	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650886	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs389663	0.82[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs4443534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56314470	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60541940	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62430987	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62430988	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62430989	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62431047	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62431051	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62431052	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9320611	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372483	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9374675	0.91[EUR][1000 genomes]
rs9387489	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9387490	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9387496	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9387497	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9401015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9401016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9401017	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9689424	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9689805	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9689889	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[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	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs210643	CARM1	trans	cerebellum	SCAN
rs210643	MCM9	cis	parietal	SCAN
rs210643	DCBLD1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117869800-117903800	Weak transcription	Spleen	Spleen
2	chr6:117869800-117904000	Weak transcription	Gastric	stomach
3	chr6:117869800-117904000	Weak transcription	Pancreas	Pancrea
4	chr6:117871600-117922600	Weak transcription	Stomach Mucosa	stomach
5	chr6:117872200-117905600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:117874600-117921400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:117876800-117919800	Weak transcription	Hela-S3	cervix
8	chr6:117877000-117903800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:117880800-117903600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:117880800-117903600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:117880800-117904000	Weak transcription	Aorta	Aorta
12	chr6:117880800-117904000	Weak transcription	Esophagus	oesophagus
13	chr6:117881800-117901600	Strong transcription	Dnd41	blood
14	chr6:117882600-117916400	Weak transcription	Small Intestine	intestine
15	chr6:117883000-117902800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:117884600-117904000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:117884600-117916200	Weak transcription	Fetal Brain Male	brain
18	chr6:117885600-117902400	Strong transcription	HSMM	muscle
19	chr6:117886600-117903600	Weak transcription	Brain Germinal Matrix	brain
20	chr6:117887600-117902000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:117887600-117922200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:117887800-117906800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:117889800-117905600	Weak transcription	Ovary	ovary
24	chr6:117890600-117912600	Weak transcription	Fetal Heart	heart
25	chr6:117890600-117918600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:117890800-117910000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:117890800-117914000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr6:117890800-117918400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:117890800-117919800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr6:117890800-117919800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:117890800-117920600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:117891000-117901400	Weak transcription	Brain Anterior Caudate	brain
33	chr6:117891000-117901800	Weak transcription	NHLF	lung
34	chr6:117891000-117903600	Weak transcription	Thymus	Thymus
35	chr6:117891000-117906800	Weak transcription	Psoas Muscle	Psoas
36	chr6:117891000-117910000	Weak transcription	NHEK	skin
37	chr6:117891000-117911200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:117891000-117920600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:117892200-117903600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr6:117892200-117918400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:117892200-117921400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr6:117892400-117910000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:117892400-117920800	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:117894200-117902200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr6:117894200-117919000	Weak transcription	Fetal Kidney	kidney
46	chr6:117894600-117910200	Weak transcription	HUVEC	blood vessel
47	chr6:117894800-117903600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:117894800-117903600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:117894800-117904000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:117894800-117909800	Weak transcription	Left Ventricle	heart

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