Variant report

Variant	rs4075861
Chromosome Location	chr1:227542811-227542812
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	chr1:227500332..227503244-chr1:227542452..227546426,3	K562	blood:
2	chr1:227538699..227541484-chr1:227541523..227544732,3	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10458380	0.81[ASN][1000 genomes]
rs10753434	0.86[ASN][1000 genomes]
rs10799412	0.86[ASN][1000 genomes]
rs10916123	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916124	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916127	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916128	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916129	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10916133	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs12022275	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023427	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12028523	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035190	0.82[ASW][hapmap]
rs12047964	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12057466	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12062358	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12081061	0.81[CEU][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12085773	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16847682	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847690	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654860	0.90[ASN][1000 genomes]
rs4075196	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4233226	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4233227	0.82[CHB][hapmap]
rs4294380	0.80[CHB][hapmap]
rs4531260	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653497	1.00[ASN][1000 genomes]
rs4653498	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs4653826	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4653828	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653831	0.92[ASN][1000 genomes]
rs59718661	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61833060	1.00[ASN][1000 genomes]
rs6690898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67343057	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72632826	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72759365	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7519870	0.99[ASN][1000 genomes]
rs7540726	0.82[ASN][1000 genomes]
rs7540833	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7541775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7553358	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7555764	0.87[ASN][1000 genomes]
rs7556096	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4075861	CCDC67	trans	parietal	SCAN
rs4075861	PGAM2	trans	parietal	SCAN
rs4075861	ARF1	cis	cerebellum	SCAN
rs4075861	CNIH4	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227539200-227545000	Weak transcription	Brain Substantia Nigra	brain
2	chr1:227539400-227544400	Weak transcription	Right Atrium	heart
3	chr1:227539400-227544400	Weak transcription	Right Ventricle	heart
4	chr1:227539400-227545000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:227539600-227544200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:227539600-227544200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:227539600-227544200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:227539600-227544200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:227539600-227544200	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:227539600-227544200	Weak transcription	HMEC	breast
11	chr1:227539600-227544200	Weak transcription	HSMM	muscle
12	chr1:227539600-227544200	Weak transcription	NH-A	brain
13	chr1:227539600-227544200	Weak transcription	NHEK	skin
14	chr1:227539600-227544200	Weak transcription	Osteobl	bone
15	chr1:227539600-227544600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:227539600-227544800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:227539800-227543600	Weak transcription	Hela-S3	cervix
18	chr1:227539800-227543800	Weak transcription	A549	lung
19	chr1:227539800-227544200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:227539800-227544200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:227539800-227544400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:227539800-227544400	Weak transcription	HSMMtube	muscle
23	chr1:227540400-227544400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:227540600-227544200	Weak transcription	Adipose Nuclei	Adipose
25	chr1:227540600-227544200	Weak transcription	Left Ventricle	heart
26	chr1:227540600-227544200	Weak transcription	Lung	lung
27	chr1:227540800-227543600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:227540800-227544200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:227540800-227544200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:227540800-227544400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:227540800-227544400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:227541200-227543600	Weak transcription	HUVEC	blood vessel
33	chr1:227541600-227543800	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr1:227542200-227543400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:227542200-227543600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:227542400-227543400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:227542400-227544400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:227542600-227547400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:227542800-227544400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr1:227542800-227544400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:227542800-227545800	Enhancers	HUES64 Cell Line	embryonic stem cell

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