Variant report

Variant	rs6426075
Chromosome Location	chr1:225637606-225637607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225636376..225639030-chr1:225641511..225643648,3	K562	blood:
2	chr1:225615892..225618526-chr1:225635437..225638461,3	K562	blood:
3	chr1:225633065..225638606-chr1:225639136..225643843,7	MCF-7	breast:
4	chr1:225615694..225617916-chr1:225635591..225638558,4	K562	blood:
5	chr1:225637530..225639456-chr1:225642105..225644098,3	K562	blood:
6	chr1:225629716..225632443-chr1:225636032..225637800,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10799310	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10799312	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10915831	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915836	0.86[ASN][1000 genomes]
rs11588279	0.92[CHB][hapmap]
rs12032961	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs12034829	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs12071529	0.84[EUR][1000 genomes]
rs12742313	0.81[ASN][1000 genomes]
rs1340865	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1340867	0.82[CHB][hapmap]
rs1764347	0.89[TSI][hapmap]
rs1890999	0.86[EUR][1000 genomes]
rs1891000	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2039620	0.82[ASN][1000 genomes]
rs2066233	0.92[CHB][hapmap]
rs2185528	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766930	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs3893032	0.92[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs4233220	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4554690	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653638	1.00[CEU][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes]
rs4653640	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs499385	0.89[TSI][hapmap]
rs499782	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs544404	0.89[TSI][hapmap]
rs6692054	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6696038	0.91[CHB][hapmap]
rs6702641	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72750896	0.83[EUR][1000 genomes]
rs7522622	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7527014	0.83[ASN][1000 genomes]
rs7527184	0.82[AMR][1000 genomes]
rs7536925	0.81[ASN][1000 genomes]
rs7548473	0.81[ASN][1000 genomes]
rs7550784	0.81[ASN][1000 genomes]
rs954534	0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6426075	C1orf95	cis	cerebellum	SCAN
rs6426075	HHIPL2	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225632200-225637800	Enhancers	Stomach Mucosa	stomach
2	chr1:225633000-225640200	Enhancers	Fetal Thymus	thymus
3	chr1:225633400-225637800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:225633600-225642000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:225633800-225637800	Enhancers	Colonic Mucosa	Colon
6	chr1:225633800-225638400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:225634200-225638000	Enhancers	Duodenum Mucosa	Duodenum
8	chr1:225634200-225642000	Weak transcription	K562	blood
9	chr1:225634400-225638200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:225634600-225638200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:225634600-225648400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:225635000-225638200	Weak transcription	Thymus	Thymus
13	chr1:225635000-225647800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:225635200-225639200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:225635200-225641200	Weak transcription	Liver	Liver
16	chr1:225635400-225638400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:225635400-225641800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:225635600-225638200	Weak transcription	Left Ventricle	heart
19	chr1:225635600-225638600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:225635600-225641600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:225635600-225642000	Weak transcription	Pancreas	Pancrea
22	chr1:225635800-225638200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:225635800-225638600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:225635800-225639800	Enhancers	Adipose Nuclei	Adipose
25	chr1:225636000-225638600	Weak transcription	Fetal Kidney	kidney
26	chr1:225636200-225637800	Enhancers	Fetal Stomach	stomach
27	chr1:225636200-225650000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:225636400-225637800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr1:225636400-225638800	Weak transcription	Brain Anterior Caudate	brain
30	chr1:225636400-225639800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:225636400-225639800	Enhancers	HMEC	breast
32	chr1:225636400-225641600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:225636400-225641600	Weak transcription	NHLF	lung
34	chr1:225636400-225642000	Weak transcription	Right Atrium	heart
35	chr1:225636600-225638200	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:225636600-225639400	Enhancers	NHEK	skin
37	chr1:225636600-225640800	Enhancers	HepG2	liver
38	chr1:225636600-225641400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:225636600-225641600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:225636600-225641800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:225636600-225642000	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:225636800-225639600	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:225637000-225637800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:225637000-225637800	Enhancers	Esophagus	oesophagus
45	chr1:225637000-225637800	Enhancers	Placenta	Placenta
46	chr1:225637000-225637800	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr1:225637000-225637800	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr1:225637000-225637800	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr1:225637000-225638000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:225637200-225637800	Enhancers	Gastric	stomach

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