Variant report

Variant	rs940136
Chromosome Location	chr4:8448992-8448993
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8442733..8444744-chr4:8447806..8449869,2	MCF-7	breast:
2	chr4:8448752..8450520-chr4:8461645..8464586,2	MCF-7	breast:
3	chr4:8442271..8445405-chr4:8446237..8450088,4	MCF-7	breast:
4	chr4:8448973..8451278-chr4:8451762..8453729,2	K562	blood:

Variant related genes	Relation type
ENSG00000087008	Chromatin interaction
ENSG00000155275	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10461079	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1357481	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1543246	0.88[ASN][1000 genomes]
rs1880023	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1880024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1916326	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1949733	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2010758	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2140337	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2386227	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450475	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2631731	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2631734	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2631735	1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[EUR][1000 genomes]
rs2631736	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631740	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631742	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2631743	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631744	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2631745	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631746	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2631754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631756	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2631758	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2631762	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2631768	0.81[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs2688219	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688223	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2688224	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688227	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688231	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2688233	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688235	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688242	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2688243	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[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];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2688247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103067	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3103069	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3103070	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3103071	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3103072	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3103099	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4696828	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447875	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6837429	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6845969	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6858542	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs868105	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs871768	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs940133	0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs940134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs940136	C4orf23	cis	cerebellum	SCAN
rs940136	C4orf6	cis	cerebellum	SCAN
rs940136	RP11-689P11.2	cis	lung	GTEx
rs940136	TBC1D14	cis	parietal	SCAN
rs940136	TRMT44	cis	Nerve Tibial	GTEx
rs940136	C4orf23	cis	parietal	SCAN
rs940136	STK32B	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8443600-8455400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:8443800-8449000	Weak transcription	Lung	lung
3	chr4:8444000-8449400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr4:8444000-8450400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:8444000-8452800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:8444200-8456800	Weak transcription	A549	lung
7	chr4:8444400-8449200	Weak transcription	Colonic Mucosa	Colon
8	chr4:8444400-8452400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:8444400-8455400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:8444600-8449400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:8444600-8452800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr4:8444600-8455800	Weak transcription	NHDF-Ad	bronchial
13	chr4:8444800-8449200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:8444800-8449800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:8444800-8452600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:8444800-8452600	Weak transcription	HUVEC	blood vessel
17	chr4:8444800-8453400	Weak transcription	Fetal Brain Male	brain
18	chr4:8444800-8458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:8445000-8449200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:8445000-8449600	Weak transcription	Fetal Thymus	thymus
21	chr4:8445000-8451000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:8445000-8452200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:8445000-8454600	Weak transcription	NH-A	brain
24	chr4:8445000-8454800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:8445000-8460800	Weak transcription	Psoas Muscle	Psoas
26	chr4:8445200-8449000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:8445200-8449200	Weak transcription	Brain Anterior Caudate	brain
28	chr4:8445200-8449200	Weak transcription	Gastric	stomach
29	chr4:8445200-8449200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:8445200-8449600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:8445200-8454600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:8445200-8454600	Weak transcription	Small Intestine	intestine
33	chr4:8445200-8461400	Weak transcription	Hela-S3	cervix
34	chr4:8445400-8449000	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:8445400-8450000	Weak transcription	GM12878-XiMat	blood
36	chr4:8445400-8450800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:8445400-8450800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:8445400-8453800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr4:8445400-8455000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:8445600-8453800	Weak transcription	Right Atrium	heart
41	chr4:8445800-8450600	Weak transcription	HMEC	breast
42	chr4:8445800-8453400	Weak transcription	Fetal Heart	heart
43	chr4:8446400-8457400	Strong transcription	Fetal Intestine Small	intestine
44	chr4:8446400-8463200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr4:8446400-8473800	Strong transcription	Fetal Stomach	stomach
46	chr4:8446600-8463600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:8446600-8463600	Strong transcription	Thymus	Thymus
48	chr4:8446600-8464600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:8446600-8473400	Strong transcription	Dnd41	blood
50	chr4:8446600-8474000	Strong transcription	Fetal Muscle Leg	muscle

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