Variant report

Variant	rs324735
Chromosome Location	chr4:76705014-76705015
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76704931..76708571-chr4:76709075..76713501,5	K562	blood:
2	chr4:76498762..76499538-chr4:76704887..76705580,2	MCF-7	breast:
3	chr4:76683893..76685556-chr4:76704376..76707290,2	K562	blood:
4	chr4:76683893..76686994-chr4:76703855..76707290,3	K562	blood:

Variant related genes	Relation type
ENSG00000138768	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10028291	0.93[ASW][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap]
rs10031352	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031616	0.83[AFR][1000 genomes]
rs10212995	0.86[ASW][hapmap]
rs10856853	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11097112	0.84[YRI][hapmap];0.92[AFR][1000 genomes]
rs11097117	0.94[ASN][1000 genomes]
rs11097121	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11097122	0.89[AFR][1000 genomes]
rs11556146	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11727895	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728073	0.89[AFR][1000 genomes]
rs11732850	0.80[ASN][1000 genomes]
rs11734358	0.87[ASN][1000 genomes]
rs11935073	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12233780	0.94[ASN][1000 genomes]
rs12498415	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12505147	0.92[ASN][1000 genomes]
rs12505149	0.92[AFR][1000 genomes]
rs12506101	0.92[ASN][1000 genomes]
rs12508200	0.84[ASN][1000 genomes]
rs12508992	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511212	0.94[ASN][1000 genomes]
rs12511575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13133144	0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs13137229	0.80[ASN][1000 genomes]
rs13145290	0.93[ASW][hapmap];0.93[LWK][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes]
rs16996019	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17000786	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17000794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17000864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs186563	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2089253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2175640	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271472	0.84[YRI][hapmap];0.89[AFR][1000 genomes]
rs28573275	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680723	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869175	0.87[AFR][1000 genomes]
rs324686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324688	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324690	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324691	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324694	0.87[TSI][hapmap]
rs324696	0.95[CEU][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324697	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324698	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324700	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324701	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324703	1.00[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]
rs324709	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs324712	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324713	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs324719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324722	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324726	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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs324727	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324730	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324731	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324734	0.87[TSI][hapmap]
rs324738	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs324740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34855591	0.81[ASN][1000 genomes]
rs4262008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610362	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4859408	0.93[ASW][hapmap];0.93[LWK][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs4859409	0.88[AFR][1000 genomes]
rs4859555	0.92[AFR][1000 genomes]
rs61603278	0.94[ASN][1000 genomes]
rs6531816	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6531901	0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs6531934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6822619	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6827016	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847333	0.93[ASW][hapmap];0.89[LWK][hapmap];0.80[AFR][1000 genomes]
rs6856162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs72858061	0.94[ASN][1000 genomes]
rs7340822	0.85[CHB][hapmap]
rs7657198	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663617	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7680729	0.91[ASN][1000 genomes]
rs7684778	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7693127	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs324735	CDKL2	cis	parietal	SCAN
rs324735	DLK2	trans	cerebellum	SCAN
rs324735	FAM47E	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76650800-76737800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:76652400-76725000	Weak transcription	Hela-S3	cervix
3	chr4:76671000-76739400	Weak transcription	Stomach Mucosa	stomach
4	chr4:76671600-76707800	Weak transcription	Right Ventricle	heart
5	chr4:76674800-76715200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:76675000-76727400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:76676400-76730600	Weak transcription	Spleen	Spleen
8	chr4:76677000-76710200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:76677000-76736200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:76685800-76719200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr4:76685800-76738400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:76687600-76716200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:76687800-76705600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:76688200-76738200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr4:76689400-76706400	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr4:76689400-76724000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:76689600-76705800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:76689800-76709200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:76691200-76713600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:76691200-76717000	Strong transcription	Placenta	Placenta
21	chr4:76691400-76715400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:76691600-76706000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr4:76691600-76706400	Strong transcription	Osteobl	bone
24	chr4:76691600-76707200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr4:76691600-76710000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:76691600-76710400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:76691800-76708600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:76691800-76716800	Strong transcription	Fetal Intestine Large	intestine
29	chr4:76692000-76706000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr4:76692000-76706000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:76692000-76706200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:76692000-76709800	Strong transcription	Fetal Thymus	thymus
33	chr4:76692000-76717400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr4:76692400-76708600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:76694800-76706600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:76695000-76708400	Strong transcription	HSMM	muscle
37	chr4:76695000-76717200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:76695200-76706000	Strong transcription	Fetal Muscle Leg	muscle
39	chr4:76695200-76709200	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:76695400-76705800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:76695400-76706400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr4:76695400-76706400	Strong transcription	Adipose Nuclei	Adipose
43	chr4:76695800-76705800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:76695800-76706000	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:76695800-76706400	Strong transcription	Fetal Lung	lung
46	chr4:76696800-76705200	Weak transcription	Pancreas	Pancrea
47	chr4:76697600-76734400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr4:76698000-76711400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr4:76698000-76711600	Weak transcription	Brain Angular Gyrus	brain
50	chr4:76698000-76721600	Weak transcription	Brain Anterior Caudate	brain

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