Variant report

Variant	rs6671751
Chromosome Location	chr1:224545784-224545785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224545456..224548563-chr1:224564069..224566245,3	K562	blood:
2	chr1:224369887..224372532-chr1:224544188..224545968,2	K562	blood:
3	chr1:224543721..224546086-chr1:224562908..224565121,2	MCF-7	breast:
4	chr1:224543329..224547108-chr1:224619239..224622996,5	MCF-7	breast:
5	chr1:224544325..224548164-chr1:224620481..224623704,4	K562	blood:
6	chr1:224514132..224518075-chr1:224542843..224545822,3	K562	blood:
7	chr1:224545747..224547349-chr1:224557974..224560385,2	K562	blood:
8	chr1:224515424..224519366-chr1:224544067..224546170,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143748	Chromatin interaction
ENSG00000143753	Chromatin interaction
ENSG00000143771	Chromatin interaction
ENSG00000143786	Chromatin interaction
ENSG00000162923	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10127813	0.95[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127953	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10128058	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10159333	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10495219	0.95[CEU][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10753465	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10753466	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10753467	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10753468	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10799569	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916606	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs10916607	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916614	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs10916616	0.95[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10916617	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10916619	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11576835	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs11577170	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11577183	0.96[EUR][1000 genomes]
rs11579952	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584247	0.96[EUR][1000 genomes]
rs11584638	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11584980	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs11586729	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs11588973	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11590658	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs11800613	0.95[CEU][hapmap];0.97[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11801436	0.95[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11801645	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11803414	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803981	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805973	0.91[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11807763	0.95[CEU][hapmap];0.97[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11807942	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811053	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12062871	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12731035	0.94[EUR][1000 genomes]
rs12731630	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12738799	0.95[CEU][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12739486	0.95[CEU][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12740255	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs12742821	0.96[EUR][1000 genomes]
rs12742989	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12743200	0.95[CEU][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12745610	0.95[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12747286	0.90[EUR][1000 genomes]
rs12751161	0.95[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12754832	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs12755338	0.84[EUR][1000 genomes]
rs12755816	0.95[CEU][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12758302	0.83[EUR][1000 genomes]
rs12758579	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12759275	0.96[EUR][1000 genomes]
rs1539207	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1544196	0.95[CEU][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16848365	0.95[CEU][hapmap];0.97[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17503938	0.90[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185684	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28434172	0.88[EUR][1000 genomes]
rs2897048	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs35011635	0.88[EUR][1000 genomes]
rs35031726	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35067427	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35169600	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35277713	0.88[EUR][1000 genomes]
rs35303987	0.88[EUR][1000 genomes]
rs35341841	0.94[EUR][1000 genomes]
rs35365551	0.84[EUR][1000 genomes]
rs35571080	0.86[EUR][1000 genomes]
rs35915186	0.82[EUR][1000 genomes]
rs35972228	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36138926	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653585	0.95[CEU][hapmap]
rs4653587	0.89[EUR][1000 genomes]
rs4654037	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55730749	0.86[EUR][1000 genomes]
rs56223447	0.96[EUR][1000 genomes]
rs6426121	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs6426123	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs6426125	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6426126	0.95[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66467176	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6663522	0.95[CEU][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6672859	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6675858	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691779	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs6693287	0.95[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6701145	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs67065875	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68037178	0.95[EUR][1000 genomes]
rs7365151	0.86[EUR][1000 genomes]
rs7512431	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7513208	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514284	0.86[CEU][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7514575	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7517754	0.95[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518109	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7519734	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522956	0.95[CEU][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7527044	0.95[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7529067	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529310	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs867362	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs885606	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9970697	0.85[EUR][1000 genomes]

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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6671751	CNIH4	cis	Adipose Subcutaneous	GTEx
rs6671751	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs6671751	CNIH4	cis	Muscle Skeletal	GTEx
rs6671751	CNIH4	cis	Esophagus Mucosa	GTEx
rs6671751	CNIH4	cis	Esophagus Muscularis	GTEx
rs6671751	CNIH4	cis	Heart Left Ventricle	GTEx
rs6671751	CNIH4	cis	Nerve Tibial	GTEx
rs6671751	CNIH4	cis	Stomach	GTEx
rs6671751	CNIH4	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224544000-224546400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:224544200-224545800	Active TSS	A549	lung
3	chr1:224544200-224546000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:224544400-224545800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:224544400-224545800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:224544400-224545800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:224544400-224545800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:224544400-224545800	Active TSS	Brain Angular Gyrus	brain
9	chr1:224544400-224545800	Active TSS	Esophagus	oesophagus
10	chr1:224544400-224545800	Active TSS	Fetal Intestine Large	intestine
11	chr1:224544400-224545800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:224544400-224545800	Active TSS	Right Ventricle	heart
13	chr1:224544400-224546000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:224544400-224546000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:224544400-224546000	Active TSS	Colonic Mucosa	Colon
16	chr1:224544600-224545800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:224544600-224546000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr1:224544800-224546000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr1:224545000-224546000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:224545000-224546000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr1:224545200-224545800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr1:224545200-224545800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:224545200-224545800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:224545200-224545800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:224545200-224545800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:224545200-224545800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:224545200-224545800	Flanking Active TSS	Liver	Liver
28	chr1:224545200-224546000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr1:224545200-224546000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr1:224545200-224546000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:224545200-224546000	Flanking Active TSS	Fetal Thymus	thymus
32	chr1:224545200-224546000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr1:224545200-224546000	Flanking Active TSS	Dnd41	blood
34	chr1:224545200-224546000	Flanking Active TSS	Osteobl	bone
35	chr1:224545200-224546200	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr1:224545200-224546200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr1:224545200-224546200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr1:224545200-224546200	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr1:224545200-224546200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr1:224545200-224546400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr1:224545200-224546600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:224545200-224555200	Weak transcription	Spleen	Spleen
43	chr1:224545400-224545800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:224545400-224545800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr1:224545400-224545800	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr1:224545400-224545800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr1:224545400-224545800	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr1:224545400-224545800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr1:224545400-224545800	Enhancers	Small Intestine	intestine
50	chr1:224545400-224545800	Flanking Active TSS	Thymus	Thymus

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