Variant report

Variant	rs11204879
Chromosome Location	chr1:151725754-151725755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:151725700-151725850	HCT-116	colon:	n/a	n/a
2	CTCF	chr1:151725680-151725970	MCF-7	breast:	n/a	n/a
3	CTCF	chr1:151725720-151725870	GM12871	blood:	n/a	n/a
4	CTCF	chr1:151725720-151725870	GM12875	blood:	n/a	n/a
5	CTCF	chr1:151725740-151725890	HMEC	breast:	n/a	n/a
6	CTCF	chr1:151725720-151725870	GM12865	blood:	n/a	n/a
7	CTCF	chr1:151725740-151725890	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr1:151725680-151725830	WERI-Rb-1	eye:	n/a	n/a
9	CTCF	chr1:151725700-151725850	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151719068..151723308-chr1:151725326..151729049,4	K562	blood:
2	chr1:151725268..151728071-chr1:151729793..151731866,2	MCF-7	breast:
3	chr1:151711448..151713959-chr1:151724394..151726703,2	K562	blood:
4	chr1:151711863..151713959-chr1:151723622..151725894,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269621	TF binding region
ENSG00000236940	TF binding region
ENSG00000236940	Chromatin interaction
ENSG00000206980	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10218531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888429	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888430	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.92[ASN][1000 genomes]
rs10888431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888432	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888433	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888434	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204881	0.89[ASN][1000 genomes]
rs11204882	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12069106	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12095851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143606	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs12758387	0.96[CEU][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs2017850	0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2096402	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs4043740	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4845339	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs4845340	0.97[EUR][1000 genomes]
rs4845542	0.92[EUR][1000 genomes]
rs61815076	0.87[EUR][1000 genomes]
rs6587615	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs6587616	0.84[EUR][1000 genomes]
rs6587617	0.89[CEU][hapmap]
rs6677429	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6692364	0.93[ASW][hapmap];0.96[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];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696250	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs7414314	0.84[EUR][1000 genomes]
rs8480	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs878775	0.80[CEU][hapmap]
rs939592	0.85[CEU][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11204879	TDRKH	cis	cerebellum	SCAN
rs11204879	TDRKH	cis	parietal	SCAN
rs11204879	BCL9	cis	cerebellum	SCAN
rs11204879	CTSK	cis	parietal	SCAN
rs11204879	GOLPH3L	cis	parietal	SCAN
rs11204879	SPRR2B	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151712800-151729400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:151712800-151731800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:151721400-151727600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:151721400-151730600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:151722400-151729200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:151722800-151729200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:151723000-151728000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:151723000-151729200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:151723400-151726800	Weak transcription	Primary T cells from cord blood	blood
10	chr1:151723400-151729000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:151723400-151730000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:151723400-151730000	Weak transcription	HSMM	muscle
13	chr1:151723800-151729400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:151723800-151730600	Weak transcription	Fetal Brain Male	brain
15	chr1:151724000-151729200	Weak transcription	Dnd41	blood
16	chr1:151724200-151727200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:151724400-151728200	Weak transcription	Liver	Liver
18	chr1:151724600-151727200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:151724800-151729200	Weak transcription	Fetal Stomach	stomach
20	chr1:151724800-151729600	Weak transcription	Brain Germinal Matrix	brain
21	chr1:151724800-151729800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:151725000-151727400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:151725000-151727800	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:151725000-151728600	Weak transcription	Fetal Brain Female	brain
25	chr1:151725200-151728000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:151725200-151728800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:151725200-151729400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:151725400-151729200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:151725400-151729600	Weak transcription	Aorta	Aorta
30	chr1:151725600-151725800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:151725600-151730000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:151725600-151730600	Weak transcription	HSMMtube	muscle

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