Variant report

Variant	rs6946179
Chromosome Location	chr7:128346398-128346399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr7:128345927-128346466	HUVEC	blood vessel:	n/a	chr7:128346108-128346119
2	PBX3	chr7:128345881-128346400	SK-N-SH	brain:	n/a	n/a
3	FOSL2	chr7:128345895-128346506	SK-N-SH	brain:	n/a	n/a
4	NFIC	chr7:128345668-128346494	SK-N-SH	brain:	n/a	n/a
5	JUN	chr7:128345762-128346413	K562	blood:	n/a	n/a
6	GATA2	chr7:128346102-128346484	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:128346237..128350299-chr7:128378242..128382310,4	K562	blood:
2	chr7:128346113..128353140-chr7:128377714..128381349,8	K562	blood:

Variant related genes	Relation type
FAM71F1	TF binding region
ENSG00000128595	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10085435	0.81[EUR][1000 genomes]
rs10224862	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233059	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10241185	0.82[EUR][1000 genomes]
rs10242806	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253131	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10259359	0.80[EUR][1000 genomes]
rs10270431	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10270985	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10274878	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10276810	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10954205	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11761312	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768485	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11771884	0.83[AMR][1000 genomes]
rs12333625	0.84[EUR][1000 genomes]
rs12535238	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536288	0.89[ASN][1000 genomes]
rs12706858	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13224613	0.84[EUR][1000 genomes]
rs13233377	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13235219	0.84[EUR][1000 genomes]
rs13237593	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521711	0.84[EUR][1000 genomes]
rs339070	1.00[ASN][1000 genomes]
rs339071	1.00[ASN][1000 genomes]
rs339074	1.00[ASN][1000 genomes]
rs339079	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339093	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34120723	0.82[EUR][1000 genomes]
rs34125589	0.80[AMR][1000 genomes]
rs34490491	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34751214	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35247963	0.87[EUR][1000 genomes]
rs35825132	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35871589	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3816421	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4289745	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55953818	0.83[AMR][1000 genomes]
rs60029447	0.83[AMR][1000 genomes]
rs6467201	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6467205	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6943737	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960296	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6961754	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6967393	0.84[EUR][1000 genomes]
rs6971819	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6972787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976879	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977126	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71546785	0.80[AMR][1000 genomes]
rs71546786	0.83[AMR][1000 genomes]
rs71548762	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776915	0.81[EUR][1000 genomes]
rs7778169	0.80[AMR][1000 genomes]
rs7778731	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7787764	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7790478	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7804472	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7810047	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811083	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9690934	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9692416	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9768808	0.87[EUR][1000 genomes]
rs9769753	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1016979	chr7:128333070-128534438	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6946179	CICP14	cis	Thyroid	GTEx
rs6946179	CICP14	cis	Muscle Skeletal	GTEx
rs6946179	RP11-274B21.10	cis	Thyroid	GTEx
rs6946179	CICP14	cis	Nerve Tibial	GTEx
rs6946179	METTL2B	cis	Artery Tibial	GTEx
rs6946179	CICP14	cis	Esophagus Muscularis	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128338600-128349000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:128339000-128358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:128344000-128348200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:128344000-128349000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:128344200-128348600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:128344400-128348600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:128344600-128347000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:128344800-128346400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr7:128344800-128346400	Bivalent Enhancer	K562	blood
10	chr7:128345200-128350200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:128345200-128350200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:128345400-128348000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:128345400-128348000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:128345400-128348400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:128345400-128348600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:128345400-128348600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:128345400-128348800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr7:128345600-128346600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:128345800-128346400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:128345800-128346400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:128345800-128346400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:128345800-128346400	Enhancers	Right Atrium	heart
23	chr7:128345800-128346400	Enhancers	NHEK	skin
24	chr7:128345800-128346600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:128345800-128346800	Enhancers	Placenta	Placenta
26	chr7:128345800-128347000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr7:128346000-128346400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:128346000-128346400	Enhancers	HMEC	breast
29	chr7:128346000-128346800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr7:128346000-128346800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:128346000-128346800	Enhancers	HUVEC	blood vessel
32	chr7:128346000-128347000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr7:128346000-128349000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:128346200-128346400	Enhancers	Spleen	Spleen
35	chr7:128346200-128350400	Weak transcription	Monocytes-CD14+_RO01746	blood

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