Variant report

Variant	rs6660716
Chromosome Location	chr1:226999183-226999184
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226998600..227001296-chr1:227008651..227010463,2	K562	blood:
2	chr1:226998001..226999981-chr1:227000720..227003139,2	MCF-7	breast:
3	chr1:226997587..227000105-chr1:227001744..227003689,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10799368	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916039	0.91[JPT][hapmap]
rs10916042	0.92[ASN][1000 genomes]
rs10916043	0.92[ASN][1000 genomes]
rs10916054	0.93[EUR][1000 genomes]
rs11405	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs1150895	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1150896	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11590925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039247	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12044509	0.92[ASN][1000 genomes]
rs12126209	0.99[EUR][1000 genomes]
rs12128150	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12130758	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12131495	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12133772	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12133818	0.98[EUR][1000 genomes]
rs12563993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12749910	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1295642	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1295645	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1295648	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1295651	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1297990	0.92[CEU][hapmap]
rs1800678	0.92[CEU][hapmap]
rs2236913	0.92[CEU][hapmap]
rs2802267	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2855563	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs34741989	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61835655	0.89[ASN][1000 genomes]
rs61835656	0.89[ASN][1000 genomes]
rs61835658	0.90[ASN][1000 genomes]
rs61837761	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61837762	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61837763	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426542	0.97[EUR][1000 genomes]
rs6426543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660109	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663555	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678134	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs743602	0.87[EUR][1000 genomes]
rs7525811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553957	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9660802	0.99[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6660716	PYCR2	cis	parietal	SCAN
rs6660716	GJC2	cis	parietal	SCAN
rs6660716	LEFTY1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226987200-227001400	Weak transcription	Right Atrium	heart
2	chr1:226989400-227002800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:226992800-227003200	Weak transcription	Lung	lung
4	chr1:226993600-227001400	Weak transcription	Thymus	Thymus
5	chr1:226994800-227007000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:226995000-227003400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:226995800-227009800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:226996600-226999200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:226996600-226999200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:226996800-226999200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:226997400-226999200	Enhancers	Brain Substantia Nigra	brain
12	chr1:226997600-227001600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:226997800-227001600	Weak transcription	Brain Anterior Caudate	brain
14	chr1:226998200-227001400	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:226998200-227002000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:226998200-227002400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:226998200-227002400	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:226998400-227001600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:226998400-227001600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:226998400-227003200	Weak transcription	Pancreas	Pancrea
21	chr1:226998600-227001400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:226998600-227001400	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:226998600-227001400	Weak transcription	Fetal Thymus	thymus
24	chr1:226998600-227001400	Weak transcription	HSMM	muscle
25	chr1:226998600-227001800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:226998600-227002000	Weak transcription	NH-A	brain
27	chr1:226998600-227002800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:226998800-227001400	Weak transcription	HSMMtube	muscle
29	chr1:226998800-227001600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:226998800-227002000	Weak transcription	Placenta	Placenta
31	chr1:226998800-227002400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:226999000-227001600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:226999000-227002400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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