Variant report

Variant	rs6666941
Chromosome Location	chr1:70646293-70646294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70643607..70646837-chr1:70686224..70688710,3	K562	blood:

Variant related genes	Relation type
ENSG00000116754	Chromatin interaction
ENSG00000228988	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1412867	0.94[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17131236	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131238	1.00[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17131241	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34121744	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35522955	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3753818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476591	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs522320	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs549843	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56299138	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56873377	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57098486	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs587567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60409157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60598073	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs610953	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61785267	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61785269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61785270	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61785272	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs632047	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs650740	0.82[CHB][hapmap]
rs651717	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs666163	1.00[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6664084	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6664480	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700543	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs676753	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74085998	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7533067	0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][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	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv870841	chr1:70612416-70696554	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6666941	SFRS11	Cis_1M	lymphoblastoid	RTeQTL
rs6666941	CTH	cis	lymphoblastoid	seeQTL
rs6666941	WLS	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70601200-70652000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr1:70603400-70648800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:70606800-70651600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:70606800-70661800	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:70607000-70670200	Weak transcription	Psoas Muscle	Psoas
6	chr1:70607000-70670400	Weak transcription	Small Intestine	intestine
7	chr1:70607200-70652600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:70607400-70655200	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:70608400-70653400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:70608800-70654800	Weak transcription	Thymus	Thymus
11	chr1:70608800-70655800	Weak transcription	Esophagus	oesophagus
12	chr1:70609200-70647600	Weak transcription	Colonic Mucosa	Colon
13	chr1:70609200-70650200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:70609400-70649800	Weak transcription	Fetal Brain Male	brain
15	chr1:70609600-70661200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:70610000-70656600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:70610000-70667800	Weak transcription	HepG2	liver
18	chr1:70610400-70650200	Weak transcription	GM12878-XiMat	blood
19	chr1:70610400-70653600	Weak transcription	Gastric	stomach
20	chr1:70610600-70669600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:70611000-70666600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:70611200-70670400	Weak transcription	Pancreas	Pancrea
23	chr1:70611400-70652800	Weak transcription	Spleen	Spleen
24	chr1:70612400-70669000	Weak transcription	HUVEC	blood vessel
25	chr1:70613000-70649200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:70613400-70658400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:70613600-70657000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:70613600-70667800	Weak transcription	Brain Angular Gyrus	brain
29	chr1:70613800-70649200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:70613800-70658000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:70614400-70651000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:70614400-70657800	Weak transcription	Fetal Kidney	kidney
33	chr1:70615000-70670000	Weak transcription	NH-A	brain
34	chr1:70615000-70670400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:70615200-70649200	Weak transcription	Left Ventricle	heart
36	chr1:70616400-70649200	Weak transcription	Fetal Lung	lung
37	chr1:70622600-70651400	Weak transcription	HMEC	breast
38	chr1:70623000-70656600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:70623000-70661600	Weak transcription	K562	blood
40	chr1:70623200-70652000	Weak transcription	Osteobl	bone
41	chr1:70624000-70650200	Weak transcription	Hela-S3	cervix
42	chr1:70624200-70648600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:70626800-70649800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:70629800-70669600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:70632600-70656800	Weak transcription	NHLF	lung
46	chr1:70634000-70670400	Weak transcription	Lung	lung
47	chr1:70634200-70658000	Weak transcription	Brain Germinal Matrix	brain
48	chr1:70634400-70649200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:70634400-70649200	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:70634400-70670200	Weak transcription	Fetal Stomach	stomach

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