Variant report

Variant	rs6692364
Chromosome Location	chr1:151730062-151730063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151729586-151730112	K562	blood:	n/a	n/a
2	POLR2A	chr1:151729177-151730192	K562	blood:	n/a	n/a
3	POLR2A	chr1:151729823-151730132	K562	blood:	n/a	n/a
4	POLR2A	chr1:151729744-151730273	K562	blood:	n/a	n/a
5	POLR2A	chr1:151729169-151730073	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:151729348-151730085	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:151729680-151730092	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:151729130-151730092	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151262059..151264776-chr1:151727556..151730221,2	K562	blood:
2	chr1:151725268..151728071-chr1:151729793..151731866,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236940	TF binding region
ENSG00000269621	Chromatin interaction
ENSG00000143373	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10218531	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888429	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888430	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.91[ASN][1000 genomes]
rs10888431	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888432	1.00[ASW][hapmap];1.00[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];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888433	1.00[ASW][hapmap];1.00[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];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888434	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204879	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]
rs11204880	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204881	0.90[ASN][1000 genomes]
rs11204882	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12069106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12095851	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12143606	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs12758387	0.92[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1781417	0.85[ASW][hapmap]
rs2017850	0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2096402	0.84[CEU][hapmap]
rs4043740	0.95[CEU][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4845339	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs4845340	0.90[EUR][1000 genomes]
rs4845542	0.98[EUR][1000 genomes]
rs61815076	0.93[EUR][1000 genomes]
rs6587615	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs6587617	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs6677429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696250	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs7414314	0.90[EUR][1000 genomes]
rs8480	1.00[ASW][hapmap];1.00[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];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939592	0.81[CEU][hapmap]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6692364	TDRKH	cis	cerebellum	SCAN
rs6692364	SPRR2B	cis	cerebellum	SCAN
rs6692364	GATAD2B	cis	cerebellum	SCAN
rs6692364	LCE1C	cis	parietal	SCAN
rs6692364	FLG2	cis	cerebellum	SCAN
rs6692364	CTSK	cis	parietal	SCAN
rs6692364	CA14	cis	cerebellum	SCAN
rs6692364	BCL9	cis	cerebellum	SCAN
rs6692364	TDRKH	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151712800-151731800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:151721400-151730600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:151723800-151730600	Weak transcription	Fetal Brain Male	brain
4	chr1:151725600-151730600	Weak transcription	HSMMtube	muscle
5	chr1:151725800-151730600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:151726000-151730400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:151726000-151730600	Weak transcription	Pancreas	Pancrea
8	chr1:151726200-151730600	Weak transcription	Primary B cells from cord blood	blood
9	chr1:151726200-151730600	Weak transcription	Esophagus	oesophagus
10	chr1:151726200-151731600	Weak transcription	Lung	lung
11	chr1:151726200-151731800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:151726400-151730600	Weak transcription	NH-A	brain
13	chr1:151726600-151730600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:151726800-151734800	Strong transcription	Primary T cells from cord blood	blood
15	chr1:151727000-151730600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:151727200-151734600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr1:151727400-151734600	Strong transcription	Brain Anterior Caudate	brain
18	chr1:151727400-151734800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr1:151727400-151735400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:151727600-151734600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:151727600-151734600	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:151727600-151734600	Strong transcription	Thymus	Thymus
23	chr1:151727600-151735000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:151727600-151735200	Weak transcription	Right Ventricle	heart
25	chr1:151727800-151730600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:151727800-151730600	Weak transcription	Fetal Heart	heart
27	chr1:151727800-151731800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:151727800-151734800	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:151728000-151730600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:151728000-151730600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:151728000-151730600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:151728000-151730800	Weak transcription	HepG2	liver
33	chr1:151728000-151733800	Weak transcription	Psoas Muscle	Psoas
34	chr1:151728000-151734600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:151728000-151734800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:151728200-151730200	Weak transcription	Fetal Lung	lung
37	chr1:151728200-151730400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:151728200-151730400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:151728200-151730600	Weak transcription	Placenta	Placenta
40	chr1:151728200-151734800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:151728200-151734800	Strong transcription	Liver	Liver
42	chr1:151728400-151730600	Weak transcription	Brain Angular Gyrus	brain
43	chr1:151728400-151730600	Weak transcription	Ovary	ovary
44	chr1:151728400-151730800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:151728400-151730800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:151728400-151733200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:151728600-151730600	Weak transcription	Fetal Kidney	kidney
48	chr1:151728600-151730600	Weak transcription	Gastric	stomach
49	chr1:151728600-151731800	Weak transcription	Left Ventricle	heart
50	chr1:151728600-151734600	Strong transcription	Fetal Brain Female	brain

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