Variant report

Variant	rs11974698
Chromosome Location	chr7:7220234-7220235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:7220051..7223731-chr7:7605300..7608795,5	K562	blood:
2	chr7:7138712..7144572-chr7:7219459..7223789,7	K562	blood:
3	chr7:7220227..7222107-chr7:7381152..7382805,2	MCF-7	breast:
4	chr7:7213763..7219997-chr7:7220116..7223880,12	MCF-7	breast:
5	chr7:7138294..7142693-chr7:7219176..7223789,9	K562	blood:

Variant related genes	Relation type
ENSG00000272894	Chromatin interaction
ENSG00000164654	Chromatin interaction
ENSG00000201218	Chromatin interaction
ENSG00000244167	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11761684	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11762665	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MKK][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11763876	0.91[ASN][1000 genomes]
rs11765592	0.87[ASN][1000 genomes]
rs11765714	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11770958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773401	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11773545	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12702586	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13224188	0.81[AFR][1000 genomes]
rs13229375	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13243458	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1432196	0.96[ASN][1000 genomes]
rs1432199	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35356155	0.81[AFR][1000 genomes]
rs35663821	0.81[AFR][1000 genomes]
rs740534	0.82[ASN][1000 genomes]
rs7803355	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1023133	chr7:6854098-7516700	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1020929	chr7:6954959-7232920	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
6	nsv464300	chr7:7040176-7368699	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv606033	chr7:7040176-7368699	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv1016369	chr7:7053923-7375567	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv1023788	chr7:7053923-7407783	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
10	nsv538720	chr7:7053923-7407783	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv1032813	chr7:7053923-7497484	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
12	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
13	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
14	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
15	nsv1032974	chr7:7145831-7393218	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
17	nsv508445	chr7:7190518-7261098	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	esv2758102	chr7:7209911-7493901	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
19	esv2759505	chr7:7209911-7493901	Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11974698	C1GALT1	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7205800-7220800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr7:7205800-7220800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr7:7211200-7220400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:7212000-7220400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr7:7212800-7220800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:7213000-7220400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:7213000-7220400	Weak transcription	Dnd41	blood
8	chr7:7213600-7220800	Enhancers	HMEC	breast
9	chr7:7216000-7220800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:7216800-7220400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr7:7216800-7220800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:7216800-7220800	Weak transcription	Adipose Nuclei	Adipose
13	chr7:7216800-7221000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:7216800-7221200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:7217000-7220400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:7217000-7220400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr7:7217000-7220400	Weak transcription	HSMMtube	muscle
18	chr7:7217000-7220400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr7:7217000-7220600	Weak transcription	Primary T cells from cord blood	blood
20	chr7:7217000-7220800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:7217000-7220800	Weak transcription	Small Intestine	intestine
22	chr7:7217000-7221000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:7217000-7221000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr7:7217200-7220400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:7217200-7220800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:7217200-7220800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:7217200-7220800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr7:7217200-7221200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr7:7217400-7220400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr7:7217400-7220600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:7217400-7220800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:7217400-7220800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:7217400-7220800	Weak transcription	Fetal Kidney	kidney
34	chr7:7217600-7220400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr7:7217600-7220800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr7:7217600-7220800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr7:7217600-7220800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr7:7217600-7220800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr7:7217600-7220800	Weak transcription	Stomach Mucosa	stomach
40	chr7:7217600-7220800	Enhancers	HepG2	liver
41	chr7:7217600-7221000	Weak transcription	NH-A	brain
42	chr7:7217800-7220400	Weak transcription	Fetal Intestine Large	intestine
43	chr7:7217800-7220600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr7:7217800-7220800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:7217800-7220800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:7217800-7220800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr7:7217800-7220800	Weak transcription	HUVEC	blood vessel
48	chr7:7217800-7221200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr7:7218000-7220400	Weak transcription	Fetal Intestine Small	intestine
50	chr7:7218600-7220400	Weak transcription	Muscle Satellite Cultured Cells	--

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